---
OA_place: repository
OA_type: green
_id: '21135'
abstract:
- lang: eng
  text: Three-dimensional (3D) microscopy data is often anisotropic with significantly
    lower resolution (up to 8x) along the z axis than along the xy axes. Computationally
    generating plausible isotropic resolution from anisotropic imaging data would
    benefit the visual analysis of large-scale volumes. This paper proposes niiv,
    a self-supervised method for isotropic reconstruction of 3D microscopy data that
    can quickly produce images at arbitrary output resolutions. The representation
    embeds a learned latent code within a neural field that describes the implicit
    higher-resolution isotropic image region. We use an attention-guided latent interpolation
    approach, which allows flexible information exchange over a local latent neighborhood.
    Under isotropic volume assumptions, we self-supervise this representation on low-/high-resolution
    lateral image pairs to reconstruct an isotropic volume from low-resolution axial
    images. We evaluate our method on simulated and real anisotropic electron (EM)
    and light microscopy (LM) data. Compared to diffusion-based baselines, niiv shows
    improved reconstruction quality (+1 dB PSNR) and is over three orders of magnitude
    faster (1,000x) to infer. Specifically, niiv reconstructs a 128^3 voxel volume
    in 2/10th of a second, renderable at varying (continuous) high resolutions for
    display. Our code is available at https://github.com/jakobtroidl/niiv-miccai.
acknowledgement: This work was supported by NIH grants 1U01NS132158 and R01HD104969.
  We thank the reviewers for their constructive feedback.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jakob
  full_name: Troidl, Jakob
  last_name: Troidl
- first_name: Yiqing
  full_name: Liang, Yiqing
  last_name: Liang
- first_name: Johanna
  full_name: Beyer, Johanna
  last_name: Beyer
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Markus
  full_name: Hadwiger, Markus
  last_name: Hadwiger
- first_name: Hanspeter
  full_name: Pfister, Hanspeter
  last_name: Pfister
- first_name: James
  full_name: Tompkin, James
  last_name: Tompkin
citation:
  ama: 'Troidl J, Liang Y, Beyer J, et al. niiv: Interactive Self-supervised Neural
    Implicit Isotropic Volume Reconstruction. In: <i>1st International Workshop on
    Efficient Medical Artificial Intelligence</i>. Vol 16318. Springer Nature; 2026:257-267.
    doi:<a href="https://doi.org/10.1007/978-3-032-13961-0_26">10.1007/978-3-032-13961-0_26</a>'
  apa: 'Troidl, J., Liang, Y., Beyer, J., Tavakoli, M., Danzl, J. G., Hadwiger, M.,
    … Tompkin, J. (2026). niiv: Interactive Self-supervised Neural Implicit Isotropic
    Volume Reconstruction. In <i>1st International Workshop on Efficient Medical Artificial
    Intelligence</i> (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature.
    <a href="https://doi.org/10.1007/978-3-032-13961-0_26">https://doi.org/10.1007/978-3-032-13961-0_26</a>'
  chicago: 'Troidl, Jakob, Yiqing Liang, Johanna Beyer, Mojtaba Tavakoli, Johann G
    Danzl, Markus Hadwiger, Hanspeter Pfister, and James Tompkin. “Niiv: Interactive
    Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” In <i>1st International
    Workshop on Efficient Medical Artificial Intelligence</i>, 16318:257–67. Springer
    Nature, 2026. <a href="https://doi.org/10.1007/978-3-032-13961-0_26">https://doi.org/10.1007/978-3-032-13961-0_26</a>.'
  ieee: 'J. Troidl <i>et al.</i>, “niiv: Interactive Self-supervised Neural Implicit
    Isotropic Volume Reconstruction,” in <i>1st International Workshop on Efficient
    Medical Artificial Intelligence</i>, Daejeon, South Korea, 2026, vol. 16318, pp.
    257–267.'
  ista: 'Troidl J, Liang Y, Beyer J, Tavakoli M, Danzl JG, Hadwiger M, Pfister H,
    Tompkin J. 2026. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume
    Reconstruction. 1st International Workshop on Efficient Medical Artificial Intelligence.
    EMA4MICCAI: Efficient Medical Artificial Intelligence, LNCS, vol. 16318, 257–267.'
  mla: 'Troidl, Jakob, et al. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic
    Volume Reconstruction.” <i>1st International Workshop on Efficient Medical Artificial
    Intelligence</i>, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:<a href="https://doi.org/10.1007/978-3-032-13961-0_26">10.1007/978-3-032-13961-0_26</a>.'
  short: J. Troidl, Y. Liang, J. Beyer, M. Tavakoli, J.G. Danzl, M. Hadwiger, H. Pfister,
    J. Tompkin, in:, 1st International Workshop on Efficient Medical Artificial Intelligence,
    Springer Nature, 2026, pp. 257–267.
conference:
  end_date: 2025-09-23
  location: Daejeon, South Korea
  name: 'EMA4MICCAI: Efficient Medical Artificial Intelligence'
  start_date: 2025-09-23
date_created: 2026-02-01T23:01:44Z
date_published: 2026-01-03T00:00:00Z
date_updated: 2026-02-16T08:50:50Z
day: '03'
department:
- _id: JoDa
doi: 10.1007/978-3-032-13961-0_26
fulldoi: https://doi.org/10.1007/978-3-032-13961-0_26
intvolume: '     16318'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2024.09.07.611785
month: '01'
oa: 1
oa_version: Preprint
page: 257-267
publication: 1st International Workshop on Efficient Medical Artificial Intelligence
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9783032139603'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/jakobtroidl/niiv-miccai
scopus_import: '1'
status: public
title: 'niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16318
year: '2026'
...
---
OA_place: repository
OA_type: gold
_id: '18697'
abstract:
- lang: eng
  text: The information-processing capability of the brain’s cellular network depends
    on the physical wiring pattern between neurons and their molecular and functional
    characteristics. Mapping neurons and resolving their individual synaptic connections
    can be achieved by volumetric imaging at nanoscale resolution with dense cellular
    labelling. Light microscopy is uniquely positioned to visualize specific molecules
    but dense, synapse-level circuit reconstruction by light microscopy has been out
    of reach due to limitations in resolution, contrast, and volumetric imaging capability.
    Here we developed light-microscopy based connectomics (LICONN). We integrated
    specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
    based segmentation and analysis of connectivity, thus directly incorporating molecular
    information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
    brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: E-Lib
article_processing_charge: No
author:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
citation:
  ama: Danzl JG, Lyudchik J, Kreuzinger C. Light-microscopy based connectomic reconstruction
    of mammalian brain tissue. 2025. doi:<a href="https://doi.org/10.15479/AT:ISTA:18697">10.15479/AT:ISTA:18697</a>
  apa: Danzl, J. G., Lyudchik, J., &#38; Kreuzinger, C. (2025). Light-microscopy based
    connectomic reconstruction of mammalian brain tissue. Institute of Science and
    Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:18697">https://doi.org/10.15479/AT:ISTA:18697</a>
  chicago: Danzl, Johann G, Julia Lyudchik, and Caroline Kreuzinger. “Light-Microscopy
    Based Connectomic Reconstruction of Mammalian Brain Tissue.” Institute of Science
    and Technology Austria, 2025. <a href="https://doi.org/10.15479/AT:ISTA:18697">https://doi.org/10.15479/AT:ISTA:18697</a>.
  ieee: J. G. Danzl, J. Lyudchik, and C. Kreuzinger, “Light-microscopy based connectomic
    reconstruction of mammalian brain tissue.” Institute of Science and Technology
    Austria, 2025.
  ista: Danzl JG, Lyudchik J, Kreuzinger C. 2025. Light-microscopy based connectomic
    reconstruction of mammalian brain tissue, Institute of Science and Technology
    Austria, <a href="https://doi.org/10.15479/AT:ISTA:18697">10.15479/AT:ISTA:18697</a>.
  mla: Danzl, Johann G., et al. <i>Light-Microscopy Based Connectomic Reconstruction
    of Mammalian Brain Tissue</i>. Institute of Science and Technology Austria, 2025,
    doi:<a href="https://doi.org/10.15479/AT:ISTA:18697">10.15479/AT:ISTA:18697</a>.
  short: J.G. Danzl, J. Lyudchik, C. Kreuzinger, (2025).
contributor:
- contributor_type: researcher
  first_name: Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- contributor_type: researcher
  first_name: Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- contributor_type: researcher
  first_name: Michal
  last_name: Januszewski
- contributor_type: researcher
  first_name: Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- contributor_type: researcher
  first_name: Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- contributor_type: researcher
  first_name: Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
- contributor_type: researcher
  first_name: Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- contributor_type: researcher
  first_name: Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- contributor_type: researcher
  first_name: Bárbara
  id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
  last_name: Oliveira
- contributor_type: researcher
  first_name: Alban
  last_name: Cenameri
- contributor_type: researcher
  first_name: Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- contributor_type: researcher
  first_name: Viren
  last_name: Jain
- contributor_type: researcher
  first_name: Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
corr_author: '1'
date_created: 2024-12-20T09:22:20Z
date_published: 2025-03-03T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '03'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.15479/AT:ISTA:18697
file:
- access_level: open_access
  checksum: d2c3efcd354f967290f91ff34dfb3cc1
  content_type: text/rtf
  creator: jdanzl
  date_created: 2025-02-28T16:50:39Z
  date_updated: 2025-02-28T16:50:39Z
  file_id: '19275'
  file_name: Readme_Data_Tavakoli_et_al_2025.rtf
  file_size: 1922
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b20cfb9b7030375f94d4b9bc5ce5cee9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:37Z
  date_updated: 2025-02-27T08:16:37Z
  file_id: '19089'
  file_name: Fig1b (1).tif
  file_size: 69884200
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2059d95e6f289cc10c970c30cd5c09a0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:36Z
  date_updated: 2025-02-27T08:16:36Z
  file_id: '19090'
  file_name: Fig1b (2).tif
  file_size: 4511994
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a259143bb581b998e9411f90403951a3
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:36Z
  date_updated: 2025-02-27T08:16:36Z
  file_id: '19091'
  file_name: Fig1b (3).tif
  file_size: 636956
  relation: main_file
  success: 1
- access_level: open_access
  checksum: e4f07b9a7a40ceac70d1c02efdaac8c0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:37Z
  date_updated: 2025-02-27T08:16:37Z
  file_id: '19092'
  file_name: Fig1b (4).tif
  file_size: 76830
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 99a9790285bea3ef600c1590e41c32ec
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:37Z
  date_updated: 2025-02-27T08:16:37Z
  file_id: '19093'
  file_name: Fig1c (1).tif
  file_size: 226548
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 4e90c8724de5a3ae7537eb5bb2ef0480
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:37Z
  date_updated: 2025-02-27T08:16:37Z
  file_id: '19094'
  file_name: Fig1c (2).tif
  file_size: 219676
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 218d009d9f15c77954ada71c507da531
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:37Z
  date_updated: 2025-02-27T08:16:37Z
  file_id: '19095'
  file_name: Fig1c (3).tif
  file_size: 219676
  relation: main_file
  success: 1
- access_level: open_access
  checksum: cb58d865959cbdffae61f47e1d41d53e
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T08:16:37Z
  date_updated: 2025-02-27T08:16:37Z
  file_id: '19096'
  file_name: Fig1c (4).tif
  file_size: 3824598
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0b8c790576fe30307050675103eafe93
  content_type: text/rtf
  creator: ckreuzin
  date_created: 2025-02-27T12:26:54Z
  date_updated: 2025-02-27T12:26:54Z
  file_id: '19097'
  file_name: Fig 2a_b_c_d_e_f.rtf
  file_size: 1510
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c9c1a66ed113c4bb74c8b2f65c5edcbb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:27:25Z
  date_updated: 2025-02-27T12:27:25Z
  file_id: '19098'
  file_name: Fig3f.tif
  file_size: 83049
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 4a822dffdca45d97d4a9b5b89aaec0f9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:27:43Z
  date_updated: 2025-02-27T12:27:43Z
  file_id: '19099'
  file_name: Fig5l (1).tif
  file_size: 640644
  relation: main_file
  success: 1
- access_level: open_access
  checksum: af130e9951a9716f40b11a5e67183fe7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:27:43Z
  date_updated: 2025-02-27T12:27:43Z
  file_id: '19100'
  file_name: Fig5l (2).tif
  file_size: 640644
  relation: main_file
  success: 1
- access_level: open_access
  checksum: cdc8829aa194593c9daf1cdaf79d9c9b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:27:55Z
  date_updated: 2025-02-27T12:27:55Z
  file_id: '19101'
  file_name: ExD2 (1).tif
  file_size: 503452
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 66808762dad2c15d0fce0dc892ce2cf0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:27:55Z
  date_updated: 2025-02-27T12:27:55Z
  file_id: '19102'
  file_name: ExD2 (2).tif
  file_size: 503452
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c7e29bf95022538a9e63149413ab2691
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:27:56Z
  date_updated: 2025-02-27T12:27:56Z
  file_id: '19103'
  file_name: ExD2 (3).tif
  file_size: 497260
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 7da1e01b4a5ec0c598b95bcf1b1746e1
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:58Z
  date_updated: 2025-02-27T12:28:58Z
  file_id: '19104'
  file_name: EXD2 overview.tif
  file_size: 2240788643
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b87093567e71c5e27007bde717017f02
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:06Z
  date_updated: 2025-02-27T12:28:06Z
  file_id: '19105'
  file_name: ExD3_a (1).tif
  file_size: 635780
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ccbfca6f0943887c202d635e1988e15c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:06Z
  date_updated: 2025-02-27T12:28:06Z
  file_id: '19106'
  file_name: ExD3_a (2).tif
  file_size: 635780
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a601cd6153f3dd3900496bd3715780dc
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:06Z
  date_updated: 2025-02-27T12:28:06Z
  file_id: '19107'
  file_name: ExD3_a overview.tif
  file_size: 8850309
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 82fe82494388f2b514e5eab08cf42567
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:06Z
  date_updated: 2025-02-27T12:28:06Z
  file_id: '19108'
  file_name: ExD3_b (1).tif
  file_size: 888645
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 6f0b4bc3cc46f9f139776b5baf608d40
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:06Z
  date_updated: 2025-02-27T12:28:06Z
  file_id: '19109'
  file_name: ExD3_b (2).tif
  file_size: 888645
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f6d984add5f2bdf4bf0c5a8d52c3dbdd
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:08Z
  date_updated: 2025-02-27T12:28:08Z
  file_id: '19110'
  file_name: ExD3_b overview.tif
  file_size: 25170991
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c508a203601d322039716d74799df4fd
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:16Z
  date_updated: 2025-02-27T12:28:16Z
  file_id: '19111'
  file_name: ExD5_a (1).tif
  file_size: 748126
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 195a02aa816058454d6fb9347834aef8
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:17Z
  date_updated: 2025-02-27T12:28:17Z
  file_id: '19112'
  file_name: ExD5_a (2).tif
  file_size: 167518
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1eb28e43902974d7f424e803e99c0234
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:17Z
  date_updated: 2025-02-27T12:28:17Z
  file_id: '19113'
  file_name: ExD5_a (3).tif
  file_size: 167518
  relation: main_file
  success: 1
- access_level: open_access
  checksum: e450c88cac136a11af8c52e4966dcb15
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:18Z
  date_updated: 2025-02-27T12:28:18Z
  file_id: '19114'
  file_name: ExD5_a (4).tif
  file_size: 25169039
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 839a53eb45926407639ccdf07a326f73
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:18Z
  date_updated: 2025-02-27T12:28:18Z
  file_id: '19115'
  file_name: ExD5_a (5).tif
  file_size: 748126
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 080703b3ee6001af8805d079f0ef101d
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:18Z
  date_updated: 2025-02-27T12:28:18Z
  file_id: '19116'
  file_name: ExD5_b (1).tif
  file_size: 5959861
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a51cca7fd7283491f09ead98bac06be8
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:30:13Z
  date_updated: 2025-02-27T12:30:13Z
  file_id: '19128'
  file_name: ExD5_b (2).tif
  file_size: 603445
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 417d4c6c4cbf4580d1b0f252ad0d1b53
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:19Z
  date_updated: 2025-02-27T12:28:19Z
  file_id: '19117'
  file_name: ExD5_b (3).tif
  file_size: 603445
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a7cfb8c48d9696f7be2068d7e5b97ec0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:19Z
  date_updated: 2025-02-27T12:28:19Z
  file_id: '19118'
  file_name: ExD5_c (1).tif
  file_size: 480392
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 4e61066979d7002bd1d5e295a0031fa6
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:20Z
  date_updated: 2025-02-27T12:28:20Z
  file_id: '19119'
  file_name: ExD5_c (2).tif
  file_size: 5947784
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2c1e59c738e9ca2cf6d474a522746bd0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:20Z
  date_updated: 2025-02-27T12:28:20Z
  file_id: '19120'
  file_name: ExD5_c (3).tif
  file_size: 480392
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 86ff0d32c6004ba817c0fb8581853f70
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:34Z
  date_updated: 2025-02-27T12:28:34Z
  file_id: '19121'
  file_name: ExD6_C (1).tif
  file_size: 25170872
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ba8c3fd2cb84bea6d0ff4b7346a1f617
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:34Z
  date_updated: 2025-02-27T12:28:34Z
  file_id: '19122'
  file_name: ExD6_C (2).tif
  file_size: 595434
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 6c235a6fc961ca5fec8e6ad90cca585b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:34Z
  date_updated: 2025-02-27T12:28:34Z
  file_id: '19123'
  file_name: ExD6_C (3).tif
  file_size: 595434
  relation: main_file
  success: 1
- access_level: open_access
  checksum: aae7959ad3571773a60c93d8fb239f0e
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:34Z
  date_updated: 2025-02-27T12:28:34Z
  file_id: '19124'
  file_name: ExD6_HT (1).tif
  file_size: 12589048
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 91d134716e3162c7a1a399729ed43b84
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:35Z
  date_updated: 2025-02-27T12:28:35Z
  file_id: '19125'
  file_name: ExD6_HT (2).tif
  file_size: 12589516
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 154e29281e9640da6a86d55a191a7684
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:36Z
  date_updated: 2025-02-27T12:28:36Z
  file_id: '19126'
  file_name: ExD6_PA (1).tif
  file_size: 12595178
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 86f22b9fd2e5b231451f6f98c9345acb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:28:36Z
  date_updated: 2025-02-27T12:28:36Z
  file_id: '19127'
  file_name: ExD6_PA (2).tif
  file_size: 12595070
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c5d8929322f3123dd03d77a51b9dc32d
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:30:55Z
  date_updated: 2025-02-27T12:30:55Z
  file_id: '19129'
  file_name: ExD7 (1).tif
  file_size: 210228181
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 12cfa75bba1c486f8127d28c114ec4bf
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:30:51Z
  date_updated: 2025-02-27T12:30:51Z
  file_id: '19130'
  file_name: ExD7 (2).tif
  file_size: 8439640
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9b4b4fde987f0585ccb2ba43ccf64ae0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:30:51Z
  date_updated: 2025-02-27T12:30:51Z
  file_id: '19131'
  file_name: ExD7 (3).tif
  file_size: 8439640
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3430b0e859cb2840078e63acca6dc5a7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:02Z
  date_updated: 2025-02-27T12:31:02Z
  file_id: '19132'
  file_name: ExD8 (1).tif
  file_size: 12583305
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8eb083751ef494d0a982110702a4e076
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:02Z
  date_updated: 2025-02-27T12:31:02Z
  file_id: '19133'
  file_name: ExD8 (2).tif
  file_size: 12583304
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9a016467f871c78cefc7c13cd71b8a23
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:03Z
  date_updated: 2025-02-27T12:31:03Z
  file_id: '19134'
  file_name: ExD8 (3).tif
  file_size: 12583296
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 719785390d3e417325673f218a03c2ae
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:03Z
  date_updated: 2025-02-27T12:31:03Z
  file_id: '19135'
  file_name: ExD8 (4).tif
  file_size: 12583307
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 65a0aee4b5c8cd3f76189e4397bd6544
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:03Z
  date_updated: 2025-02-27T12:31:03Z
  file_id: '19136'
  file_name: ExD8 (5).tif
  file_size: 12583307
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 667753716b7148878a0b512ddc2074b4
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:03Z
  date_updated: 2025-02-27T12:31:03Z
  file_id: '19137'
  file_name: ExD8 (6).tif
  file_size: 12583286
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 61eb5fc89cbacc3bb027919139b3a4ab
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:03Z
  date_updated: 2025-02-27T12:31:03Z
  file_id: '19138'
  file_name: ExD8 (7).tif
  file_size: 12583305
  relation: main_file
  success: 1
- access_level: open_access
  checksum: eed374ceb917f66b0e9cf4ee3aed0eba
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:03Z
  date_updated: 2025-02-27T12:31:03Z
  file_id: '19139'
  file_name: ExD8 (8).tif
  file_size: 12583264
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 51d3c92bffe30a6ee417a42d24c42449
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:04Z
  date_updated: 2025-02-27T12:31:04Z
  file_id: '19140'
  file_name: ExD8 (9).tif
  file_size: 12583305
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a451c488fca7772e55d534e65f739a5d
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:32:26Z
  date_updated: 2025-02-27T12:32:26Z
  file_id: '19141'
  file_name: ExD9_a.tif
  file_size: 2637707980
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2b671ae3857517cc2493d95435eb5017
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:12Z
  date_updated: 2025-02-27T12:31:12Z
  file_id: '19142'
  file_name: ExD9_b (1).tif
  file_size: 5931874
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5b0a6d2fbd3a4790e42d64ddf082ac44
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:31:13Z
  date_updated: 2025-02-27T12:31:13Z
  file_id: '19143'
  file_name: ExD9_b (2).png
  file_size: 5574502
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 93b1ca9fe6689f972466ca7021333a2b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:13Z
  date_updated: 2025-02-27T12:31:13Z
  file_id: '19144'
  file_name: ExD9_c (1).tif
  file_size: 936816
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 087a6e5cd69ed279f4135e5acbcf0243
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:14Z
  date_updated: 2025-02-27T12:31:14Z
  file_id: '19145'
  file_name: ExD9_c (2).tif
  file_size: 9971050
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 055512e172d8c0b3f552ecdcf62d8913
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:31:14Z
  date_updated: 2025-02-27T12:31:14Z
  file_id: '19146'
  file_name: ExD9_c (3).tif
  file_size: 12589300
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0c49d7bae8d7ce058d9339d2acb5108a
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:35:44Z
  date_updated: 2025-02-27T12:35:44Z
  file_id: '19155'
  file_name: ExD10_a (1).tif
  file_size: 12587348
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 108d47b78fd5af3a751319b8a0f336c5
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:32:38Z
  date_updated: 2025-02-27T12:32:38Z
  file_id: '19147'
  file_name: ExD10_a (2).tif
  file_size: 12587344
  relation: main_file
  success: 1
- access_level: open_access
  checksum: dab543a769dd05cfbd66c8bc5877decf
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:32:39Z
  date_updated: 2025-02-27T12:32:39Z
  file_id: '19148'
  file_name: ExD10_a (3).tif
  file_size: 622780
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 31feb7fcc156ba1f62c9c18c7adee1bd
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:32:39Z
  date_updated: 2025-02-27T12:32:39Z
  file_id: '19149'
  file_name: ExD10_a (4).tif
  file_size: 424064
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 069fa6237648dee9080bc779ae8bb7ab
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:32:39Z
  date_updated: 2025-02-27T12:32:39Z
  file_id: '19150'
  file_name: ExD10_c.png
  file_size: 695657
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 774a892849e024ee079e14d456908529
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:32:39Z
  date_updated: 2025-02-27T12:32:39Z
  file_id: '19151'
  file_name: ExD10_d (1).png
  file_size: 2510928
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 4f6f50fb534e7419189b82fc2b2359e8
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:32:39Z
  date_updated: 2025-02-27T12:32:39Z
  file_id: '19152'
  file_name: ExD10_d (2).png
  file_size: 975236
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 03ae30c2aa151892778e1d5be85c5722
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:32:40Z
  date_updated: 2025-02-27T12:32:40Z
  file_id: '19153'
  file_name: ExD10_e.png
  file_size: 714346
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a973fcca17ee02a0377a3494cafb66e9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:32:45Z
  date_updated: 2025-02-27T12:32:45Z
  file_id: '19154'
  file_name: ExD10_h.tif
  file_size: 239750348
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 270a780148d7bde70bcaabeeb8188559
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:23Z
  date_updated: 2025-02-27T12:36:23Z
  file_id: '19156'
  file_name: SF2 (1).tif
  file_size: 1096875
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f095b4b71c027734f10d91dad1a90911
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:24Z
  date_updated: 2025-02-27T12:36:24Z
  file_id: '19157'
  file_name: SF2 (2).tif
  file_size: 12588982
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3d635b68a0790297d8e1c854924a0e4b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:24Z
  date_updated: 2025-02-27T12:36:24Z
  file_id: '19158'
  file_name: SF2 (3).tif
  file_size: 1096897
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 233f4c55114dbf4fff623775ac7629ed
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:24Z
  date_updated: 2025-02-27T12:36:24Z
  file_id: '19159'
  file_name: SF2 (4).tif
  file_size: 12583306
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a86fc86d60b7a43f60ed204eac15ae9e
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:24Z
  date_updated: 2025-02-27T12:36:24Z
  file_id: '19160'
  file_name: SF2 (5).tif
  file_size: 1091221
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 732a94d766c59c5bc55bfb572c24b672
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:24Z
  date_updated: 2025-02-27T12:36:24Z
  file_id: '19161'
  file_name: SF2 (6).tif
  file_size: 12588974
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2a566be2ea4c9fa81d078832bce4c230
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:24Z
  date_updated: 2025-02-27T12:36:24Z
  file_id: '19162'
  file_name: SF2 (7).tif
  file_size: 1096889
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f262512298c9c8ca3d9e00dcd3a86b44
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:25Z
  date_updated: 2025-02-27T12:36:25Z
  file_id: '19163'
  file_name: SF2 (8).tif
  file_size: 12588960
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 40ce5647c948013a5f5442fdc7ac0ad2
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:36Z
  date_updated: 2025-02-27T12:36:36Z
  file_id: '19164'
  file_name: SF3 (1).tif
  file_size: 12589182
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 54f91d6ba3eb8e32779705e2eff261d3
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:36Z
  date_updated: 2025-02-27T12:36:36Z
  file_id: '19165'
  file_name: SF3 (2).tif
  file_size: 12589224
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ce8aa0f3bb62f1f29d138707cb6ced3c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:36Z
  date_updated: 2025-02-27T12:36:36Z
  file_id: '19166'
  file_name: SF3 (3).tif
  file_size: 12589178
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 00169473fb4fe3d28b38755a4757bc62
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:40Z
  date_updated: 2025-02-27T12:36:40Z
  file_id: '19167'
  file_name: SF3 (4).tif
  file_size: 12589180
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2e3304c513266b6d88fdcdd950e5b1c7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:40Z
  date_updated: 2025-02-27T12:36:40Z
  file_id: '19168'
  file_name: SF3 (5).tif
  file_size: 12589270
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 19ca076e8bc48758af33f689d5b3fece
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:45Z
  date_updated: 2025-02-27T12:36:45Z
  file_id: '19169'
  file_name: SF3 (6).tif
  file_size: 12583264
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f1257eb05a38cb93c07deb98ac6bacdb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:45Z
  date_updated: 2025-02-27T12:36:45Z
  file_id: '19170'
  file_name: SF3 (7).tif
  file_size: 12589292
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ba6747859b2c7564b1c6fd826ed1d16e
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:49Z
  date_updated: 2025-02-27T12:36:49Z
  file_id: '19171'
  file_name: SF3 (8).tif
  file_size: 12589318
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b7b9a7cb86b74ed201b3e7f2ace5699c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:49Z
  date_updated: 2025-02-27T12:36:49Z
  file_id: '19172'
  file_name: SF3 (9).tif
  file_size: 12589530
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ebd6ecf4e7054de8661df83045e0a24c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:09Z
  date_updated: 2025-02-27T12:37:09Z
  file_id: '19173'
  file_name: SF3 (10).tif
  file_size: 12589334
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0269d65803ad587ae5d12d67df645f8b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:54Z
  date_updated: 2025-02-27T12:36:54Z
  file_id: '19174'
  file_name: SF3 (11).tif
  file_size: 12589540
  relation: main_file
  success: 1
- access_level: open_access
  checksum: cd43ef86a3853e1b18da109f50d4d8ac
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:58Z
  date_updated: 2025-02-27T12:36:58Z
  file_id: '19175'
  file_name: SF3 (12).tif
  file_size: 12589296
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 77509629a7d63427fe188cd893174c50
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:58Z
  date_updated: 2025-02-27T12:36:58Z
  file_id: '19176'
  file_name: SF3 (13).tif
  file_size: 12589300
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5b2a4870ada42b714a8d0cb3b0a22897
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:59Z
  date_updated: 2025-02-27T12:36:59Z
  file_id: '19177'
  file_name: SF3 (14).tif
  file_size: 12589228
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d45667253f1fc955141b92e71c3ec0f1
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:36:59Z
  date_updated: 2025-02-27T12:36:59Z
  file_id: '19178'
  file_name: SF3 (15).tif
  file_size: 12589230
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 82e507681c2a8ee6a5fb5ebcbcb2eda1
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:34Z
  date_updated: 2025-02-27T12:37:34Z
  file_id: '19179'
  file_name: SF4_d (1).tif
  file_size: 12595602
  relation: main_file
  success: 1
- access_level: open_access
  checksum: edda9a389955107a15c762df2c1bc80b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:34Z
  date_updated: 2025-02-27T12:37:34Z
  file_id: '19180'
  file_name: SF4_d (2).tif
  file_size: 12583305
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2455e23b33bab231ab3b94bb31ffff8b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:34Z
  date_updated: 2025-02-27T12:37:34Z
  file_id: '19181'
  file_name: SF4_d (3).tif
  file_size: 12595602
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5970d5fe32278b3c0fdb2345d22ede22
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:34Z
  date_updated: 2025-02-27T12:37:34Z
  file_id: '19182'
  file_name: SF4_d (4).tif
  file_size: 12583305
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8b19af3b6dafb364e437373beb2c8249
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:35Z
  date_updated: 2025-02-27T12:37:35Z
  file_id: '19183'
  file_name: SF4_d (5).tif
  file_size: 12583293
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5948ca9e8cd4431d301829f185648e98
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:35Z
  date_updated: 2025-02-27T12:37:35Z
  file_id: '19184'
  file_name: SF4_d (6).tif
  file_size: 12595630
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 89f4b99ea59b28132380b573ac6872b7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:35Z
  date_updated: 2025-02-27T12:37:35Z
  file_id: '19185'
  file_name: SF4_d (7).tif
  file_size: 12595652
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 37fb13a610da23d59fc8eba640417844
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:35Z
  date_updated: 2025-02-27T12:37:35Z
  file_id: '19186'
  file_name: SF4_d (8).tif
  file_size: 12595554
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 59355dcf56e7caca0c7ab5896d6eee19
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:50Z
  date_updated: 2025-02-27T12:37:50Z
  file_id: '19187'
  file_name: SF5 (1).tif
  file_size: 12589366
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 02b045794b183ca0f1a3fb7746742b11
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:50Z
  date_updated: 2025-02-27T12:37:50Z
  file_id: '19188'
  file_name: SF5 (2).tif
  file_size: 12587012
  relation: main_file
  success: 1
- access_level: open_access
  checksum: e5dddad8cdca618c0cb7aa5f1b1d6f4a
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:56Z
  date_updated: 2025-02-27T12:37:56Z
  file_id: '19189'
  file_name: SF5 (3).tif
  file_size: 12589322
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 51a51d33c07f18777279c36498694048
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:37:56Z
  date_updated: 2025-02-27T12:37:56Z
  file_id: '19190'
  file_name: SF5 (4).tif
  file_size: 12589322
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f923ceac728d5ccfdfbb828615f13cbc
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:03Z
  date_updated: 2025-02-27T12:38:03Z
  file_id: '19191'
  file_name: SF5 (5).tif
  file_size: 12589322
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 15ab0e44297bf05ad0b033a00377bc9f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:03Z
  date_updated: 2025-02-27T12:38:03Z
  file_id: '19192'
  file_name: SF5 (6).tif
  file_size: 12589020
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f79330486ce56e11e1e1e44e7425e40e
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:11Z
  date_updated: 2025-02-27T12:38:11Z
  file_id: '19193'
  file_name: SF5 (7).tif
  file_size: 12589020
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 970e48a64b8414590606074355b67857
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:11Z
  date_updated: 2025-02-27T12:38:11Z
  file_id: '19194'
  file_name: SF5 (8).tif
  file_size: 12589372
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d1f671671c23159ad33d1d5ea33f84e4
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:18Z
  date_updated: 2025-02-27T12:38:18Z
  file_id: '19195'
  file_name: SF5 (9).tif
  file_size: 12589372
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3e7f08d4e4c72fc5455fc5a8cb11a9eb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:18Z
  date_updated: 2025-02-27T12:38:18Z
  file_id: '19196'
  file_name: SF5 (10).tif
  file_size: 12589366
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0fa65d9519b84ca6cac7767928f47620
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:38:27Z
  date_updated: 2025-02-27T12:38:27Z
  file_id: '19197'
  file_name: SF6_a.tif
  file_size: 1415036
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 41250d19f197453bc558d72a39523e40
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:38:28Z
  date_updated: 2025-02-27T12:38:28Z
  file_id: '19198'
  file_name: SF6_b.png
  file_size: 14771950
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 7ad4f1a30c7953aea60e4b5830eb00c1
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:38:28Z
  date_updated: 2025-02-27T12:38:28Z
  file_id: '19199'
  file_name: SF6_c.png
  file_size: 29541400
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a542e3ae50144025482e5fa6727594d6
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19200'
  file_name: SF7_a (1).tif
  file_size: 12583284
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f6ed6317a6d4586d5f456ca8b423f357
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:47Z
  date_updated: 2025-02-27T12:40:47Z
  file_id: '19201'
  file_name: SF7_a (2).tif
  file_size: 971691
  relation: main_file
  success: 1
- access_level: open_access
  checksum: da6aef7d3b8434c7ea7e7118377cd6cb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:47Z
  date_updated: 2025-02-27T12:40:47Z
  file_id: '19202'
  file_name: SF7_a (3).tif
  file_size: 971691
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0fdaca32872449bdd4773f25fedce0c2
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19203'
  file_name: SF7_a (4).tif
  file_size: 12583284
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 593636fa0c65b77d9909abce3bae27e6
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19204'
  file_name: SF7_b (1).tif
  file_size: 971689
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 008754d1e50a7f17c04ea57f3065b889
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19205'
  file_name: SF7_b (2).tif
  file_size: 971689
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 33c60d97c526f9f8f585b91255f0c9fb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19206'
  file_name: SF7_b (3).tif
  file_size: 12583282
  relation: main_file
  success: 1
- access_level: open_access
  checksum: cdb164e16c7e9b8e81baff00570e1beb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19207'
  file_name: SF7_b (4).tif
  file_size: 12583282
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b406c3f975b6ee62e4a69c36a8659395
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19208'
  file_name: SF7_c (1).tif
  file_size: 971719
  relation: main_file
  success: 1
- access_level: open_access
  checksum: baaf68d9c42824d2152ce347903a9e52
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:49Z
  date_updated: 2025-02-27T12:40:49Z
  file_id: '19209'
  file_name: SF7_c (2).tif
  file_size: 12583312
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a54fa646e45ead1eca8de2cb828b6efa
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:48Z
  date_updated: 2025-02-27T12:40:48Z
  file_id: '19210'
  file_name: SF7_c (3).tif
  file_size: 971719
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f35b92e63a88d7dcb29399205f509058
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:49Z
  date_updated: 2025-02-27T12:40:49Z
  file_id: '19211'
  file_name: SF7_c (4).tif
  file_size: 12583312
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f625e76556a9274e95962cc03b69c6ce
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:49Z
  date_updated: 2025-02-27T12:40:49Z
  file_id: '19212'
  file_name: SF7_d (1).tif
  file_size: 971721
  relation: main_file
  success: 1
- access_level: open_access
  checksum: dd38206d764413f1969dea862d0a775e
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:49Z
  date_updated: 2025-02-27T12:40:49Z
  file_id: '19213'
  file_name: SF7_d (2).tif
  file_size: 12583313
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 891705e5dd2bcc4b761f9fe1e01fe5eb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:49Z
  date_updated: 2025-02-27T12:40:49Z
  file_id: '19214'
  file_name: SF7_d (3).tif
  file_size: 971721
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c0ad4758bfe9b10df96545c76ac70ae6
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:40:49Z
  date_updated: 2025-02-27T12:40:49Z
  file_id: '19215'
  file_name: SF7_d (4).tif
  file_size: 12583313
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f28181e59bdee004afab0d2526918892
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:44Z
  date_updated: 2025-02-27T12:45:44Z
  file_id: '19216'
  file_name: SF8 (1).tif
  file_size: 12594788
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 45ac190192a5067be7c21a5fd2155a16
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:44Z
  date_updated: 2025-02-27T12:45:44Z
  file_id: '19217'
  file_name: SF8 (2).tif
  file_size: 12594804
  relation: main_file
  success: 1
- access_level: open_access
  checksum: df5a2f23c83ee70d29def18624700228
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:44Z
  date_updated: 2025-02-27T12:45:44Z
  file_id: '19218'
  file_name: SF8 (3).tif
  file_size: 12594768
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 4d7fe6b7d73527449cbadc99c6438c73
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:44Z
  date_updated: 2025-02-27T12:45:44Z
  file_id: '19219'
  file_name: SF8 (4).tif
  file_size: 12594796
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 96c36e0b7c0a58163a67d8bbbab93b3f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:44Z
  date_updated: 2025-02-27T12:45:44Z
  file_id: '19220'
  file_name: SF8 (5).tif
  file_size: 12594808
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 68f6de9a8e37adf6c826cb0da6bb9761
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:45Z
  date_updated: 2025-02-27T12:45:45Z
  file_id: '19221'
  file_name: SF8 (6).tif
  file_size: 12594788
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3ded92c972cf4693929ba34af17cc05f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:45Z
  date_updated: 2025-02-27T12:45:45Z
  file_id: '19222'
  file_name: SF8 (7).tif
  file_size: 12594790
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b5273316902e3568be63bbced5a6bad1
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:45Z
  date_updated: 2025-02-27T12:45:45Z
  file_id: '19223'
  file_name: SF8 (8).tif
  file_size: 12594782
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8af6262e2f9652d25fa029981ade9de9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:45Z
  date_updated: 2025-02-27T12:45:45Z
  file_id: '19224'
  file_name: SF8 (9).tif
  file_size: 12594778
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d643c481d2eccd5f67fb2d27223068bf
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:45Z
  date_updated: 2025-02-27T12:45:45Z
  file_id: '19225'
  file_name: SF8 (10).tif
  file_size: 12594782
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 6d3af95382f070bb63567fbf6b3f9477
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:45Z
  date_updated: 2025-02-27T12:45:45Z
  file_id: '19226'
  file_name: SF8 (11).tif
  file_size: 12594790
  relation: main_file
  success: 1
- access_level: open_access
  checksum: de12b11a75ee3fa775f144e11b68e6ed
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:46Z
  date_updated: 2025-02-27T12:45:46Z
  file_id: '19227'
  file_name: SF8 (12).tif
  file_size: 12594774
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9b79caefb934a8280adcf21b5bbf35ac
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:46Z
  date_updated: 2025-02-27T12:45:46Z
  file_id: '19228'
  file_name: SF8 (13).tif
  file_size: 12594778
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8e9442cdbd92fd61aacac52c23ca6bec
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:46Z
  date_updated: 2025-02-27T12:45:46Z
  file_id: '19229'
  file_name: SF8 (14).tif
  file_size: 12594790
  relation: main_file
  success: 1
- access_level: open_access
  checksum: e42c08a6325e82d508221e896bd4f210
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:46Z
  date_updated: 2025-02-27T12:45:46Z
  file_id: '19230'
  file_name: SF8 (15).tif
  file_size: 12594782
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 04657cd0f303f99009cb1c5d4c61551c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:58Z
  date_updated: 2025-02-27T12:45:58Z
  file_id: '19231'
  file_name: SF9_a (1).tif
  file_size: 12589358
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 512247c4f80abeafe17438584f23e09b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:58Z
  date_updated: 2025-02-27T12:45:58Z
  file_id: '19232'
  file_name: SF9_a (2).tif
  file_size: 977761
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3c85543205b21d49dbd99edbc455fc32
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:58Z
  date_updated: 2025-02-27T12:45:58Z
  file_id: '19233'
  file_name: SF9_a (3).tif
  file_size: 12589346
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3cb358e1abafb929493bba73bfef88a4
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:58Z
  date_updated: 2025-02-27T12:45:58Z
  file_id: '19234'
  file_name: SF9_a (4).tif
  file_size: 977781
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d025b195001165d7a1d44af9ad631ab9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19235'
  file_name: SF9_a (5).tif
  file_size: 12589366
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3f2fb7ce9bf45cfadce35115c12099fd
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19236'
  file_name: SF9_a (6).tif
  file_size: 977773
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 6fbe1dc7c358f988280c4f8ef04f5be9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19237'
  file_name: SF9_b (1).tif
  file_size: 977781
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c02b2420d26ec644e86c569ede14c5ef
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19238'
  file_name: SF9_b (2).tif
  file_size: 12589366
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0ed660389a060890edb85249d468a014
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19239'
  file_name: SF9_b (3).tif
  file_size: 977769
  relation: main_file
  success: 1
- access_level: open_access
  checksum: cabf39d2b5d35cd3e5854b3b16001e08
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19240'
  file_name: SF9_b (4).tif
  file_size: 12589354
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d81c3fce4bd6e2e0109f62efb2b54959
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19241'
  file_name: SF9_b (5).tif
  file_size: 977871
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 374f2e897f46f6feac9feca0fa8394cd
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:45:59Z
  date_updated: 2025-02-27T12:45:59Z
  file_id: '19242'
  file_name: SF9_b (6).tif
  file_size: 12589456
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 84a880d60f767cfe0665ea2ec595c8d7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:27Z
  date_updated: 2025-02-27T12:46:27Z
  file_id: '19243'
  file_name: SF11.tif
  file_size: 827856876
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d18add0f9f824700d0f53d2191466300
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:38Z
  date_updated: 2025-02-27T12:46:38Z
  file_id: '19244'
  file_name: SF12_a (1).tif
  file_size: 3828230
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 042d241d8b3080c8c5ff0a2dbda4a48f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:38Z
  date_updated: 2025-02-27T12:46:38Z
  file_id: '19245'
  file_name: SF12_a (2).tif
  file_size: 160112
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 955d474f43d115fedca614ed6602215f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:38Z
  date_updated: 2025-02-27T12:46:38Z
  file_id: '19246'
  file_name: SF12_a (3).tif
  file_size: 3828230
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 325f940b56634b1c33e491dcc58b3404
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:38Z
  date_updated: 2025-02-27T12:46:38Z
  file_id: '19247'
  file_name: SF12_a (4).tif
  file_size: 160112
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1b5524fb3d54489b04afe9f2f7cfebb9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:39Z
  date_updated: 2025-02-27T12:46:39Z
  file_id: '19248'
  file_name: SF12_b (1).tif
  file_size: 3821356
  relation: main_file
  success: 1
- access_level: open_access
  checksum: bacb9f4b367c2425df02ad392028e574
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:39Z
  date_updated: 2025-02-27T12:46:39Z
  file_id: '19249'
  file_name: SF12_b (2).tif
  file_size: 3821356
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5cb107bed602073a51a534ceb4c81362
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:39Z
  date_updated: 2025-02-27T12:46:39Z
  file_id: '19250'
  file_name: SF12_b (3).tif
  file_size: 3821356
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 26a07d639182a4189650f4c7dba90865
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:39Z
  date_updated: 2025-02-27T12:46:39Z
  file_id: '19251'
  file_name: SF12_b (4).tif
  file_size: 3821356
  relation: main_file
  success: 1
- access_level: open_access
  checksum: eba866000a286254545c3f6868f69b9f
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:46:51Z
  date_updated: 2025-02-27T12:46:51Z
  file_id: '19252'
  file_name: SF18_a (1).png
  file_size: 1245061
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8e6c94f552e9dbc34cd0b3853df8d015
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:51Z
  date_updated: 2025-02-27T12:46:51Z
  file_id: '19253'
  file_name: SF18_a (2).tif
  file_size: 60892
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 079d6c3e2459c71ed27bc3baafa47843
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:51Z
  date_updated: 2025-02-27T12:46:51Z
  file_id: '19254'
  file_name: SF18_a (3).tif
  file_size: 60892
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 22602da6be439acf8c3dfbb78fcc4400
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:51Z
  date_updated: 2025-02-27T12:46:51Z
  file_id: '19255'
  file_name: SF18_b (1).tif
  file_size: 12583312
  relation: main_file
  success: 1
- access_level: open_access
  checksum: eed1e333701f9085d69d5239e8719112
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:51Z
  date_updated: 2025-02-27T12:46:51Z
  file_id: '19256'
  file_name: SF18_b (2).tif
  file_size: 811600
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2215b02b1b947caf92e1bbe7185d06e1
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:46:51Z
  date_updated: 2025-02-27T12:46:51Z
  file_id: '19257'
  file_name: SF18_b (3).tif
  file_size: 811600
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 292e06efed5701eae8e83e02ed7a6e22
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:47:31Z
  date_updated: 2025-02-27T12:47:31Z
  file_id: '19258'
  file_name: SF20.tif
  file_size: 1068146032
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 32cbaee7cb8e3ce9385d716b7a54a4bc
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:48:36Z
  date_updated: 2025-02-27T12:48:36Z
  file_id: '19259'
  file_name: SF23 (1).png
  file_size: 219654
  relation: main_file
  success: 1
- access_level: open_access
  checksum: e0bbf151a4bd261a5cb1c00bed59777d
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:48:36Z
  date_updated: 2025-02-27T12:48:36Z
  file_id: '19260'
  file_name: SF23 (2).png
  file_size: 1941088
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 73ed6c45b7db745252b61d24f8c40f6f
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:48:36Z
  date_updated: 2025-02-27T12:48:36Z
  file_id: '19261'
  file_name: SF23 (3).png
  file_size: 238170
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c871ee6bc9d16b551582ec22b8e1a3bb
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:48:36Z
  date_updated: 2025-02-27T12:48:36Z
  file_id: '19262'
  file_name: SF23 (4).png
  file_size: 2026158
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 448a0397c431153bdf63b0844842feb9
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:48:36Z
  date_updated: 2025-02-27T12:48:36Z
  file_id: '19263'
  file_name: SF23 (5).png
  file_size: 262037
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b35f44db5058569ec21550b369beec4b
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:48:36Z
  date_updated: 2025-02-27T12:48:36Z
  file_id: '19264'
  file_name: SF23 (6).png
  file_size: 2052749
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5dcac37bab7e128a04ba9cdb9b34164f
  content_type: image/png
  creator: ckreuzin
  date_created: 2025-02-27T12:49:07Z
  date_updated: 2025-02-27T12:49:07Z
  file_id: '19265'
  file_name: SF23_overview.png
  file_size: 80062038
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 032c7c52f36298252cc0b19b83ea0648
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:49:50Z
  date_updated: 2025-02-27T12:49:50Z
  file_id: '19266'
  file_name: SF24 (1).tif
  file_size: 121784120
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5867b6b999d0c3d91354d92ba0d6c30b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:49:50Z
  date_updated: 2025-02-27T12:49:50Z
  file_id: '19267'
  file_name: SF24 (2).tif
  file_size: 121784062
  relation: main_file
  success: 1
- access_level: open_access
  checksum: bbf1267c8030894e846f2dc95a955014
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-27T12:51:29Z
  date_updated: 2025-02-27T12:51:29Z
  file_id: '19268'
  file_name: SF25.tif
  file_size: 2995439929
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3db644adb7181eef3181e1c418856741
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-28T09:07:23Z
  date_updated: 2025-02-28T09:07:23Z
  file_id: '19269'
  file_name: LICONN_gephyrin_test.tif
  file_size: 2400199306
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0d716ad1249be4de51e79b6d832340b9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-02-28T09:15:48Z
  date_updated: 2025-02-28T09:15:48Z
  file_id: '19270'
  file_name: LICONN_test_dataset.tif
  file_size: 588107137
  relation: main_file
  success: 1
file_date_updated: 2025-02-28T16:50:39Z
fulldoi: https://doi.org/10.15479/AT:ISTA:18697
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
  link:
  - description: Original datasets of large size (>10GB) and datasets in zarr/n5/ims/npz
      format are provided via this external link.
    relation: research_data
    url: https://pub.ista.ac.at/group_danzl/data/LICONN/
  record:
  - id: '19704'
    relation: used_in_publication
    status: public
status: public
title: Light-microscopy based connectomic reconstruction of mammalian brain tissue
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
_id: '18837'
abstract:
- lang: eng
  text: Super-resolution methods provide far better spatial resolution than the optical
    diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
    they have yet to attain widespread use in plants, largely due to plants’ challenging
    optical properties. Expansion microscopy improves effective resolution by isotropically
    increasing the physical distances between sample structures while preserving relative
    spatial arrangements and clearing the sample. However, its application to plants
    has been hindered by the rigid, mechanically cohesive structure of plant tissues.
    Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
    thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
    conventional microscopy. Our results highlight the microtubule cytoskeleton organization
    and interaction between molecularly defined cellular constituents. Combining PlantEx
    with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
    and visualize the complex organization of subcellular organelles from intact tissues
    by example of the densely packed COPI-coated vesicles associated with the Golgi
    apparatus and put these into a cellular structural context. Our results show that
    expansion microscopy can be applied to increase effective imaging resolution in
    Arabidopsis root specimens.
article_processing_charge: No
author:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
citation:
  ama: Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution
    expansion microscopy in plant roots.” 2025. doi:<a href="https://doi.org/10.15479/AT:ISTA:18837">10.15479/AT:ISTA:18837</a>
  apa: Danzl, J. G., &#38; Kreuzinger, C. (2025). Research Data for the publication
    “Super-resolution expansion microscopy in plant roots.” Institute of Science and
    Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:18837">https://doi.org/10.15479/AT:ISTA:18837</a>
  chicago: Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication
    ‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science
    and Technology Austria, 2025. <a href="https://doi.org/10.15479/AT:ISTA:18837">https://doi.org/10.15479/AT:ISTA:18837</a>.
  ieee: J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution
    expansion microscopy in plant roots.’” Institute of Science and Technology Austria,
    2025.
  ista: Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution
    expansion microscopy in plant roots’, Institute of Science and Technology Austria,
    <a href="https://doi.org/10.15479/AT:ISTA:18837">10.15479/AT:ISTA:18837</a>.
  mla: Danzl, Johann G., and Caroline Kreuzinger. <i>Research Data for the Publication
    “Super-Resolution Expansion Microscopy in Plant Roots.”</i> Institute of Science
    and Technology Austria, 2025, doi:<a href="https://doi.org/10.15479/AT:ISTA:18837">10.15479/AT:ISTA:18837</a>.
  short: J.G. Danzl, C. Kreuzinger, (2025).
contributor:
- contributor_type: researcher
  first_name: Michelle C
  id: 35A03822-F248-11E8-B48F-1D18A9856A87
  last_name: Gallei
  orcid: 0000-0003-1286-7368
- contributor_type: researcher
  first_name: Sven M
  id: 45812BD4-F248-11E8-B48F-1D18A9856A87
  last_name: Truckenbrodt
- contributor_type: researcher
  first_name: Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- contributor_type: researcher
  first_name: Syamala
  id: F8660870-D756-11E9-98C5-34DFE5697425
  last_name: Inumella
- contributor_type: researcher
  first_name: Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- contributor_type: researcher
  first_name: Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- contributor_type: researcher
  first_name: Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- contributor_type: researcher
  first_name: Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- contributor_type: researcher
  first_name: Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
- contributor_type: researcher
  first_name: Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
- contributor_type: researcher
  first_name: Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
- contributor_type: researcher
  first_name: Alexander J
  id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
  last_name: Johnson
  orcid: 0000-0002-2739-8843
- contributor_type: researcher
  first_name: Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- contributor_type: researcher
  first_name: Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- contributor_type: researcher
  first_name: Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
corr_author: '1'
date_created: 2025-01-13T09:51:29Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-06-10T08:30:20Z
department:
- _id: JoDa
doi: 10.15479/AT:ISTA:18837
file:
- access_level: open_access
  checksum: a522d476ca1106163abb403ee156f6d0
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:09:15Z
  date_updated: 2025-03-07T10:09:15Z
  file_id: '19312'
  file_name: Fig 1D+2D PlantEx.tif
  file_size: 588707932
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2d0e8279e85821de946fa8dbc4ed8134
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:29:22Z
  date_updated: 2025-03-07T10:29:22Z
  file_id: '19313'
  file_name: Fig 1D+2D Pre-expansion.tif
  file_size: 786998434
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9b965e160fb7ec9900606994fe0c3045
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:31:59Z
  date_updated: 2025-03-07T10:31:59Z
  file_id: '19314'
  file_name: Fig 1E PlantEx.tif
  file_size: 108411
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 38857ce7d0b8c4b71937ca60eef539b3
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:32:02Z
  date_updated: 2025-03-07T10:32:02Z
  file_id: '19315'
  file_name: Fig 1E Pre-expansion.tif
  file_size: 114825
  relation: main_file
  success: 1
- access_level: open_access
  checksum: fbadff70783e9c045df7aba7b5b2087c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:32:06Z
  date_updated: 2025-03-07T10:32:06Z
  file_id: '19316'
  file_name: Fig 1G PlantEx.tif
  file_size: 1816371
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d240605f1c2d94da98e5205725ce0d9a
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:32:16Z
  date_updated: 2025-03-07T10:32:16Z
  file_id: '19317'
  file_name: Fig 1G Pre-expansion.tif
  file_size: 915960
  relation: main_file
  success: 1
- access_level: open_access
  checksum: fe491eaccfe4adef56fa26c078060f00
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:32:22Z
  date_updated: 2025-03-07T10:32:22Z
  file_id: '19318'
  file_name: Fig 1H PlantEx.tif
  file_size: 766038
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 58b7bdd4588ae8548e802a71b3d25106
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:32:27Z
  date_updated: 2025-03-07T10:32:27Z
  file_id: '19319'
  file_name: Fig 1H Pre-expansion.tif
  file_size: 783535
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f86caf84d9d074789a616a707fa432c4
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:34:58Z
  date_updated: 2025-03-07T10:34:58Z
  file_id: '19320'
  file_name: Fig 2A PlantEx.tif
  file_size: 84170613
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 4c19c5ba90920a328a7a9c387042aa74
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:42:47Z
  date_updated: 2025-03-07T10:42:47Z
  file_id: '19321'
  file_name: Fig 2A Pre-expansion.tif
  file_size: 132788281
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ade4bb575af39c71d014042694ea45db
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:47:13Z
  date_updated: 2025-03-07T10:47:13Z
  file_id: '19322'
  file_name: Fig 2B PlantEx.tif
  file_size: 11570499
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 589ef451a3ccad4dca2751768c038d8b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:48:11Z
  date_updated: 2025-03-07T10:48:11Z
  file_id: '19323'
  file_name: Fig 2B Pre-expansion.tif
  file_size: 158352613
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 55ce09fb986334b0a92b04fcf1f94070
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:53:19Z
  date_updated: 2025-03-07T10:53:19Z
  file_id: '19324'
  file_name: Fig 2C PlantEx.tif
  file_size: 551565370
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d5db31a647b51aaed05908b5768e2c5c
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:55:44Z
  date_updated: 2025-03-07T10:55:44Z
  file_id: '19325'
  file_name: Fig 2C Pre-expansion.tif
  file_size: 237209144
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 93deb3bc7cbd6aef3d7e097a6b09688f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:58:44Z
  date_updated: 2025-03-07T10:58:44Z
  file_id: '19326'
  file_name: Fig 3A+SF4 PlantEx.tif
  file_size: 344621773
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 88680e7cd05f34d307a152c0a4e208f7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T10:59:39Z
  date_updated: 2025-03-07T10:59:39Z
  file_id: '19327'
  file_name: Fig 3A+SF4 Pre-expansion.tif
  file_size: 99299335
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 7e217d23c05a9a1a61455733a25fd622
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:35Z
  date_updated: 2025-03-07T11:00:35Z
  file_id: '19328'
  file_name: Fig 3B PlantEx.tif
  file_size: 7686824
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 902547dc8c550e460be5744fec9b7015
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:38Z
  date_updated: 2025-03-07T11:00:38Z
  file_id: '19329'
  file_name: Fig 3B Pre-expansion.tif
  file_size: 1491129
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 15dc0c1648fe1fd950030d7a30d1c731
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:47Z
  date_updated: 2025-03-07T11:00:47Z
  file_id: '19330'
  file_name: Fig 4A-B PlantEx-STED.tif
  file_size: 750976
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 240b34120bf876926aa05f702844acfb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:47Z
  date_updated: 2025-03-07T11:00:47Z
  file_id: '19331'
  file_name: Fig 4A-B PlantEx.tif
  file_size: 750976
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f2918750d292cba1c218845df1ea8b90
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:53Z
  date_updated: 2025-03-07T11:00:53Z
  file_id: '19332'
  file_name: Fig 4D FWHM2D-1.tif
  file_size: 5559605
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d1456dfbfe956ff9223730d756c5d848
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:55Z
  date_updated: 2025-03-07T11:00:55Z
  file_id: '19333'
  file_name: Fig 4D FWHM2D-2.tif
  file_size: 5559591
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a3e30f9618e892a4891f3bd7f1da1d83
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:57Z
  date_updated: 2025-03-07T11:00:57Z
  file_id: '19334'
  file_name: Fig 4D FWHM2D-4.tif
  file_size: 3555591
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ea95c2127c6e380e5deaed4312ecbc0f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:56Z
  date_updated: 2025-03-07T11:00:56Z
  file_id: '19335'
  file_name: Fig 4D FWHM2D-5.tif
  file_size: 546745
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1c9a6c44bf9496edea5d5fdcee2025eb
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:58Z
  date_updated: 2025-03-07T11:00:58Z
  file_id: '19336'
  file_name: Fig 4D FWHM2D-7.tif
  file_size: 3559515
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 607517b081335689779cd942a8f3c03a
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:00:59Z
  date_updated: 2025-03-07T11:00:59Z
  file_id: '19337'
  file_name: Fig 4D FWHM2D-8.tif
  file_size: 3559515
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f5b9145a467e6f41e21cc00dbfc05768
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:10Z
  date_updated: 2025-03-07T11:01:10Z
  file_id: '19338'
  file_name: Fig 4D FWHM2D-3.tif
  file_size: 5559607
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f313225115f3cf8876bd9cbad57da30f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:14Z
  date_updated: 2025-03-07T11:01:14Z
  file_id: '19339'
  file_name: Fig 4D FWHM2D-6.tif
  file_size: 843837
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b4f9a8d7eea64701f7fa673f0856a01b
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:29Z
  date_updated: 2025-03-07T11:01:29Z
  file_id: '19340'
  file_name: Fig 4E PlantEx-STED.tif
  file_size: 48215
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b4f68e70cfe0d95fcbdb3e592c46feb4
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:29Z
  date_updated: 2025-03-07T11:01:29Z
  file_id: '19341'
  file_name: Fig 4E PlantEx.tif
  file_size: 48215
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f767f2a583ba76c9ad5f81e38dd251d2
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:57Z
  date_updated: 2025-03-07T11:01:57Z
  file_id: '19342'
  file_name: Fig 4F FWHM3D-1.tif
  file_size: 31147914
  relation: main_file
  success: 1
- access_level: open_access
  checksum: fedec925ee7f8b603619f11f46969e29
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:46Z
  date_updated: 2025-03-07T11:01:46Z
  file_id: '19343'
  file_name: Fig 4F FWHM3D-2.tif
  file_size: 17311922
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 5959b072a0ad244cd14c957bc887ecd3
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:53Z
  date_updated: 2025-03-07T11:01:53Z
  file_id: '19344'
  file_name: Fig 4F FWHM3D-3.tif
  file_size: 10734416
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9397f0fc30f4671f64ff0aac5a4efeb4
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:55Z
  date_updated: 2025-03-07T11:01:55Z
  file_id: '19345'
  file_name: Fig 4F FWHM3D-4.tif
  file_size: 6776213
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c69ca5e2f28c8f4ab5b2d6f3bdb779d5
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:01:56Z
  date_updated: 2025-03-07T11:01:56Z
  file_id: '19346'
  file_name: Fig 4F FWHM3D-5.tif
  file_size: 6776212
  relation: main_file
  success: 1
- access_level: open_access
  checksum: aca23c64368ce670a4427813998319d8
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:12Z
  date_updated: 2025-03-07T11:03:12Z
  file_id: '19347'
  file_name: Fig 4G-I+SF8 PlantEx-STED.tif
  file_size: 6768975
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 77df5be8348f62e95a61f11c650b1239
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:18Z
  date_updated: 2025-03-07T11:03:18Z
  file_id: '19348'
  file_name: Fig 4J.tif
  file_size: 16939717
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b16759a063e47f170317864e1cfe7091
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:27Z
  date_updated: 2025-03-07T11:03:27Z
  file_id: '19349'
  file_name: Fig 5A.tif
  file_size: 9994358
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 0a03ceb130161d6b655fcab3bc65f05a
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:29Z
  date_updated: 2025-03-07T11:03:29Z
  file_id: '19350'
  file_name: Fig 5B.tif
  file_size: 16676433
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 72639e7d1c64d4a3a2ebad8f52d0b90f
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:35Z
  date_updated: 2025-03-07T11:03:35Z
  file_id: '19351'
  file_name: Fig 5C.tif
  file_size: 16676513
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 34f15999da729ae8c7949ec83970ff2d
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:34Z
  date_updated: 2025-03-07T11:03:34Z
  file_id: '19352'
  file_name: Fig 5D.tif
  file_size: 11064413
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 6efbd7af82f1cf5671b144b1d0a404b3
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:37Z
  date_updated: 2025-03-07T11:03:37Z
  file_id: '19353'
  file_name: Fig 5E slice.tif
  file_size: 44989
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 53a964be82125e9ba8e4565d06a018a9
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:03:39Z
  date_updated: 2025-03-07T11:03:39Z
  file_id: '19354'
  file_name: Fig 5E.tif
  file_size: 21467202
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 7ae6240c0860f3421ac69e06ed3c4fa6
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:05:55Z
  date_updated: 2025-03-07T11:05:55Z
  file_id: '19355'
  file_name: SF 3-1.tif
  file_size: 62931594
  relation: main_file
  success: 1
- access_level: open_access
  checksum: fa32e1ce1dbfaf416a3c65239c662802
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:06:32Z
  date_updated: 2025-03-07T11:06:32Z
  file_id: '19356'
  file_name: SF 3-2.tif
  file_size: 91463394
  relation: main_file
  success: 1
- access_level: open_access
  checksum: d82fd1acafd37fa9d9bfe265b1c52547
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:07:45Z
  date_updated: 2025-03-07T11:07:45Z
  file_id: '19357'
  file_name: SF5.tif
  file_size: 156454296
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2accd7b5cb49fb307884ade8b62d6051
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:07:58Z
  date_updated: 2025-03-07T11:07:58Z
  file_id: '19358'
  file_name: SF6 PlantEx.tif
  file_size: 641808
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 85efa71a36f5219550fc04cee6d87cc7
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:08:03Z
  date_updated: 2025-03-07T11:08:03Z
  file_id: '19359'
  file_name: SF6 PlantEx-STED.tif
  file_size: 5761790
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 02e32d2cf4b6aa0491b36f3b1b404517
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:08:49Z
  date_updated: 2025-03-07T11:08:49Z
  file_id: '19360'
  file_name: SF8_2.tif
  file_size: 6768975
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f6ad4696fb9f702d4d7a5411aefa87da
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:09:01Z
  date_updated: 2025-03-07T11:09:01Z
  file_id: '19361'
  file_name: SF8_3.tif
  file_size: 6768975
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 55580709fd705702a590ebbeb0e0f918
  content_type: image/tiff
  creator: ckreuzin
  date_created: 2025-03-07T11:09:13Z
  date_updated: 2025-03-07T11:09:13Z
  file_id: '19362'
  file_name: SF8_4.tif
  file_size: 6768975
  relation: main_file
  success: 1
file_date_updated: 2025-03-07T11:09:13Z
fulldoi: https://doi.org/10.15479/AT:ISTA:18837
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '19003'
    relation: used_in_publication
    status: public
status: public
title: Research Data for the publication "Super-resolution expansion microscopy in
  plant roots"
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19704'
abstract:
- lang: eng
  text: The information-processing capability of the brain’s cellular network depends
    on the physical wiring pattern between neurons and their molecular and functional
    characteristics. Mapping neurons and resolving their individual synaptic connections
    can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular
    labelling. Light microscopy is uniquely positioned to visualize specific molecules,
    but dense, synapse-level circuit reconstruction by light microscopy has been out
    of reach, owing to limitations in resolution, contrast and volumetric imaging
    capability. Here we describe light-microscopy-based connectomics (LICONN). We
    integrated specifically engineered hydrogel embedding and expansion with comprehensive
    deep-learning-based segmentation and analysis of connectivity, thereby directly
    incorporating molecular information into synapse-level reconstructions of brain
    tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological
    experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank S. Dorkenwald and P. Li for critical reading of the manuscript,
  S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge
  support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific
  Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge
  funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D.
  and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft
  für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s
  Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions
  Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation
  programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open
  access funding provided by Institute of Science and Technology (IST Austria).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Michał
  full_name: Januszewski, Michał
  last_name: Januszewski
- first_name: Vitali
  full_name: Vistunou, Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Bárbara
  full_name: Oliveira, Bárbara
  id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
  last_name: Oliveira
- first_name: Alban
  full_name: Cenameri, Alban
  id: 9ac8f577-2357-11eb-997a-e566c5550886
  last_name: Cenameri
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Viren
  full_name: Jain, Viren
  last_name: Jain
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic
    reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a
    href="https://doi.org/10.1038/s41586-025-08985-1">10.1038/s41586-025-08985-1</a>
  apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
    N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction
    of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href="https://doi.org/10.1038/s41586-025-08985-1">https://doi.org/10.1038/s41586-025-08985-1</a>
  chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
    Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based
    Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer
    Nature, 2025. <a href="https://doi.org/10.1038/s41586-025-08985-1">https://doi.org/10.1038/s41586-025-08985-1</a>.
  ieee: M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction
    of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410,
    2025.
  ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
    J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
    JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain
    tissue. Nature. 642, 398–410.
  mla: Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction
    of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp.
    398–410, doi:<a href="https://doi.org/10.1038/s41586-025-08985-1">10.1038/s41586-025-08985-1</a>.
  short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
    J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
    V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.
corr_author: '1'
date_created: 2025-05-18T22:02:51Z
date_published: 2025-06-12T00:00:00Z
date_updated: 2026-10-02T09:59:44Z
day: '12'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: Bio
- _id: GaNo
doi: 10.1038/s41586-025-08985-1
ec_funded: 1
external_id:
  isi:
  - '001483477000001'
  pmid:
  - '40335689'
file:
- access_level: open_access
  checksum: ebc99d7108e728f46db0a009292675ef
  content_type: application/pdf
  creator: dernst
  date_created: 2025-07-03T06:55:20Z
  date_updated: 2025-07-03T06:55:20Z
  file_id: '19959'
  file_name: 2025_Nature_Tavakoli.pdf
  file_size: 133201290
  relation: main_file
  success: 1
file_date_updated: 2025-07-03T06:55:20Z
fulldoi: https://doi.org/10.1038/s41586-025-08985-1
has_accepted_license: '1'
intvolume: '       642'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 398-410
pmid: 1
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
  grant_number: '101044865'
  name: Toward an understanding of the brain interstitial system and the extracellular
    proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication: Nature
publication_identifier:
  eissn:
  - 1476-4687
  issn:
  - 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - description: News on ISTA website
    relation: press_release
    url: https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/
  record:
  - id: '18697'
    relation: research_data
    status: public
  - id: '18677'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Light-microscopy-based connectomic reconstruction of mammalian brain tissue
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 642
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18879'
abstract:
- lang: eng
  text: 'Our brain has remarkable computational power, generating sophisticated behaviors,
    storing memories over an individual’s lifetime, and producing higher cognitive
    functions. However, little of our neuroscience knowledge covers the human brain.
    Is this organ truly unique, or is it a scaled version of the extensively studied
    rodent brain? Combining multicellular patch-clamp recording with expansion-based
    superresolution microscopy and full-scale modeling, we determined the cellular
    and microcircuit properties of the human hippocampal CA3 region, a fundamental
    circuit for memory storage. In contrast to neocortical networks, human hippocampal
    CA3 displayed sparse connectivity, providing a circuit architecture that maximizes
    associational power. Human synapses showed unique reliability, high precision,
    and long integration times, exhibiting both species- and circuit-specific properties.
    Together with expanded neuronal numbers, these circuit characteristics greatly
    enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit
    properties of the human hippocampus and begin to unravel the inner workings of
    our most complex organ. '
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: ScienComp
acknowledgement: We thank Florian Marr for excellent technical assistance, Christina
  Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor
  Asenov for development of the transportation box for human brain tissue, Tim Vogels
  for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann
  for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript
  editing. This research was supported by the Scientific Services Units (SSUs) of
  ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and
  Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop,
  and Scientific Computing. We are particularly grateful to the patient donors for
  their support of this project and also acknowledge the excellent support of the
  Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger
  and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division
  of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha
  Feucht, and Ekaterina Pataraia for their clinical care of the patients included
  in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample
  donors for their support of this research. The project received funding from the
  European Research Council (ERC) under the European Union’s Horizon 2020 research
  and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie
  Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund
  (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian
  Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship
  (to A.N.-O.).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jake
  full_name: Watson, Jake
  id: 63836096-4690-11EA-BD4E-32803DDC885E
  last_name: Watson
  orcid: 0000-0002-8698-3823
- first_name: Victor M
  full_name: Vargas Barroso, Victor M
  id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
  last_name: Vargas Barroso
- first_name: Rebecca
  full_name: Morse, Rebecca
  id: ceb89ae7-dc8d-11ea-abe3-da3301d0eab4
  last_name: Morse
- first_name: Andrea C
  full_name: Navas Olivé, Andrea C
  id: 739d26c9-52e8-11ee-8d72-f14d3893b4ce
  last_name: Navas Olivé
  orcid: 0000-0002-9280-8597
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Matthias
  full_name: Tomschik, Matthias
  last_name: Tomschik
- first_name: Karl
  full_name: Rössler, Karl
  last_name: Rössler
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
citation:
  ama: Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific
    functional connectivity rules for efficient associative memory. <i>Cell</i>. 2025;188(2):501-514.e18.
    doi:<a href="https://doi.org/10.1016/j.cell.2024.11.022">10.1016/j.cell.2024.11.022</a>
  apa: Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli,
    M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional
    connectivity rules for efficient associative memory. <i>Cell</i>. Cell Press.
    <a href="https://doi.org/10.1016/j.cell.2024.11.022">https://doi.org/10.1016/j.cell.2024.11.022</a>
  chicago: Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé,
    Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M
    Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for
    Efficient Associative Memory.” <i>Cell</i>. Cell Press, 2025. <a href="https://doi.org/10.1016/j.cell.2024.11.022">https://doi.org/10.1016/j.cell.2024.11.022</a>.
  ieee: J. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity
    rules for efficient associative memory,” <i>Cell</i>, vol. 188, no. 2. Cell Press,
    p. 501–514.e18, 2025.
  ista: Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG,
    Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional
    connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18.
  mla: Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity
    Rules for Efficient Associative Memory.” <i>Cell</i>, vol. 188, no. 2, Cell Press,
    2025, p. 501–514.e18, doi:<a href="https://doi.org/10.1016/j.cell.2024.11.022">10.1016/j.cell.2024.11.022</a>.
  short: J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli,
    J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18.
corr_author: '1'
date_created: 2025-01-26T23:01:49Z
date_published: 2025-01-23T00:00:00Z
date_updated: 2026-10-20T08:20:04Z
day: '23'
ddc:
- '570'
department:
- _id: JoDa
- _id: PeJo
- _id: GradSch
doi: 10.1016/j.cell.2024.11.022
ec_funded: 1
external_id:
  isi:
  - '001408395600001'
  pmid:
  - '39667938'
file:
- access_level: open_access
  checksum: d5a818edc32d249cdf75e1bb5b70a4b7
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-27T08:46:33Z
  date_updated: 2025-01-27T08:46:33Z
  file_id: '18884'
  file_name: 2025_Cell_Watson.pdf
  file_size: 14082343
  relation: main_file
  success: 1
file_date_updated: 2025-01-27T08:46:33Z
fulldoi: https://doi.org/10.1016/j.cell.2024.11.022
has_accepted_license: '1'
intvolume: '       188'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 501-514.e18
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '692692'
  name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
  call_identifier: H2020
  grant_number: '101026635'
  name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
- _id: 8d9195e9-16d5-11f0-9cad-d075be887a1e
  grant_number: PAT 4178023
  name: Synaptic networks of human brain
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
  name: NOMIS Fellowship Program
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
  record:
  - id: '18688'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Human hippocampal CA3 uses specific functional connectivity rules for efficient
  associative memory
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19795'
abstract:
- lang: eng
  text: Super-resolution microscopy often entails long acquisition times of minutes
    to hours. Since drifts during the acquisition adversely affect data quality, active
    sample stabilization is commonly used for some of these techniques to reach their
    full potential. Although drifts in the lateral plane can often be corrected after
    acquisition, this is not always possible or may come with drawbacks. Therefore,
    it is appealing to stabilize sample position in three dimensions (3D) during acquisition.
    Various schemes for active sample stabilization have been demonstrated previously,
    with some reaching sub-nanometer stability in 3D. Here, we present a scheme for
    active drift correction that delivers the nanometer-scale 3D stability demanded
    by state-of-the-art super-resolution techniques and is straightforward to implement
    compared to previous schemes capable of reaching this level of stabilization precision.
    Using a refined algorithm that can handle various types of reference structure,
    without sparse signal peaks being mandatory, we stabilized sample position to
    ∼1 nm in 3D using objective lenses both with high and low numerical aperture.
    Our implementation requires only the addition of a simple widefield imaging path
    and we provide an open-source control software with graphical user interface to
    facilitate easy adoption of the module. Finally, we demonstrate how this has the
    potential to enhance data collection for diffraction-limited and super-resolution
    imaging techniques using single-molecule localization microscopy and cryo-confocal
    imaging as showcases.
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: LifeSc
acknowledgement: 'We acknowledge expert support by ISTA’s scientific service units,
  including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support
  Facility. This work has been made possible in part by CZI grant DAF2021-234754 and
  grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative
  DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989)
  (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following
  sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian
  Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions
  Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral
  fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship
  LT000557/2018 (W.J.).'
article_number: '100211'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
- first_name: Nikolai
  full_name: Semenov, Nikolai
  id: e64d39c7-72ef-11ef-b75a-ee3046860d1b
  last_name: Semenov
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Manjunath
  full_name: Javoor, Manjunath
  id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
  last_name: Javoor
  orcid: 0000-0003-2311-2112
- first_name: Bettina
  full_name: Zens, Bettina
  id: 45FD126C-F248-11E8-B48F-1D18A9856A87
  last_name: Zens
  orcid: 0000-0002-9561-1239
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Marek
  full_name: Suplata, Marek
  id: EE8452B8-C26A-11E9-B157-E80CE6697425
  last_name: Suplata
- first_name: Wiebke
  full_name: Jahr, Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
  orcid: 0000-0003-0201-2315
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Andreas
  full_name: Wartak, Andreas
  id: 60aaa06c-3de5-11eb-9e53-baa88e955dcb
  last_name: Wartak
- first_name: Florian Km
  full_name: Schur, Florian Km
  id: 48AD8942-F248-11E8-B48F-1D18A9856A87
  last_name: Schur
  orcid: 0000-0003-4790-8078
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization
    on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2).
    doi:<a href="https://doi.org/10.1016/j.bpr.2025.100211">10.1016/j.bpr.2025.100211</a>
  apa: Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas,
    N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer
    scale for optical microscopy. <i>Biophysical Reports</i>. Cell Press. <a href="https://doi.org/10.1016/j.bpr.2025.100211">https://doi.org/10.1016/j.bpr.2025.100211</a>
  chicago: Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor,
    Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D
    Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical
    Reports</i>. Cell Press, 2025. <a href="https://doi.org/10.1016/j.bpr.2025.100211">https://doi.org/10.1016/j.bpr.2025.100211</a>.
  ieee: J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on
    the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol.
    5, no. 2. Cell Press, 2025.
  ista: Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N,
    Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025.
    Image-based 3D active sample stabilization on the nanometer scale for optical
    microscopy. Biophysical Reports. 5(2), 100211.
  mla: Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the
    Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no.
    2, 100211, Cell Press, 2025, doi:<a href="https://doi.org/10.1016/j.bpr.2025.100211">10.1016/j.bpr.2025.100211</a>.
  short: J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas,
    M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl,
    Biophysical Reports 5 (2025).
corr_author: '1'
date_created: 2025-06-08T22:01:22Z
date_published: 2025-06-11T00:00:00Z
date_updated: 2026-10-20T08:55:34Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: FlSc
- _id: EM-Fac
doi: 10.1016/j.bpr.2025.100211
ec_funded: 1
file:
- access_level: open_access
  checksum: 4018c833f25a3ad3b57e3577fed70334
  content_type: application/pdf
  creator: dernst
  date_created: 2025-06-10T07:24:46Z
  date_updated: 2025-06-10T07:24:46Z
  file_id: '19802'
  file_name: 2025_BiophysicalReports_Vorlaufer.pdf
  file_size: 7238179
  relation: main_file
  success: 1
file_date_updated: 2025-06-10T07:24:46Z
fulldoi: https://doi.org/10.1016/j.bpr.2025.100211
has_accepted_license: '1'
intvolume: '         5'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
  grant_number: CZI01
  name: CryoMinflux-guided in-situ molecular census and structure determination
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
  grant_number: LT00057
  name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Biophysical Reports
publication_identifier:
  eissn:
  - 2667-0747
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
  record:
  - id: '20206'
    relation: dissertation_contains
    status: public
  - id: '22744'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Image-based 3D active sample stabilization on the nanometer scale for optical
  microscopy
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2025'
...
---
OA_place: publisher
_id: '20206'
abstract:
- lang: eng
  text: "The internal structure of biomolecules and their organization in higher-order
    arrangements are key factors governing the working principles of biological systems.
    Bioimaging has successfully revealed arrangements across relevant spatial scales.
    For example, cryo-electron tomography has become widely used for analyzing biomolecular
    structures in situ due to its comprehensive structural visualization of near-natively
    preserved samples, and its capability of sub-nm resolution via averaging. However,
    the identification of molecules within crowded cellular environments is often
    hindered by low contrast. Fluorescence microscopy, on the other hand, routinely
    visualizes specifically labeled targets at single-molecule contrast against essentially
    zero background. Moreover, it provides comparatively high throughput and is amenable
    to multiplexing. Due to this complementarity, combining datasets from both modalities
    acquired on the same region via correlative light and electron microscopy can
    reveal novel types of information. \r\nThe spatial scale at which information
    can be extracted depends on imaging resolution and correlation accuracy. Since
    diffraction of light limits the resolution of conventional fluorescence microscopy
    to few hundreds of nanometers, reaching the full potential of correlative imaging
    requires super-resolution approaches. Performing imaging at cryogenic temperature
    preserves structures in a near-native state and minimizes distortions between
    the fluorescence and the electron microscopy datasets. Implementations of this
    concept have achieved correlation on the scale of cellular organelles or bacterial
    domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule
    scale by improving cryo-super-resolution microscopy, and devising a refined image
    correlation workflow. As part of this project, I constructed a microscopy setup
    and adopted it for super-resolution fluorescence microscopy at room temperature
    and cryogenic conditions. I explored different cryo-stages and acquisition strategies.
    Specifically, I developed a new scheme for correcting sample drift, thus increasing
    mechanical stability during microscopy acquisitions.\r\n"
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: Bio
acknowledgement: "The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI:
  https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised
  fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989),
  as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary
  Project Committee. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
citation:
  ama: Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in
    situ structure analysis. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20206">10.15479/AT-ISTA-20206</a>
  apa: Vorlaufer, J. (2025). <i>Construction of a cryo-super-resolution microscope
    to guide in situ structure analysis</i>. Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/AT-ISTA-20206">https://doi.org/10.15479/AT-ISTA-20206</a>
  chicago: Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to
    Guide in Situ Structure Analysis.” Institute of Science and Technology Austria,
    2025. <a href="https://doi.org/10.15479/AT-ISTA-20206">https://doi.org/10.15479/AT-ISTA-20206</a>.
  ieee: J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide
    in situ structure analysis,” Institute of Science and Technology Austria, 2025.
  ista: Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide
    in situ structure analysis. Institute of Science and Technology Austria.
  mla: Vorlaufer, Jakob. <i>Construction of a Cryo-Super-Resolution Microscope to
    Guide in Situ Structure Analysis</i>. Institute of Science and Technology Austria,
    2025, doi:<a href="https://doi.org/10.15479/AT-ISTA-20206">10.15479/AT-ISTA-20206</a>.
  short: J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide
    in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-22T08:12:55Z
date_published: 2025-08-25T00:00:00Z
date_updated: 2026-10-20T08:55:33Z
day: '25'
ddc:
- '621'
- '535'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/AT-ISTA-20206
file:
- access_level: closed
  checksum: 191db3367c19c9b32b65f4bc3a7c19de
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: jvorlauf
  date_created: 2025-08-25T13:49:55Z
  date_updated: 2025-08-25T13:49:55Z
  file_id: '20228'
  file_name: 2025_Vorlaufer_Jakob_Thesis.docx
  file_size: 39735535
  relation: source_file
- access_level: open_access
  checksum: 104400e6036921569610230c1d4899dc
  content_type: application/pdf
  creator: jvorlauf
  date_created: 2025-08-25T13:49:56Z
  date_updated: 2025-08-25T13:49:56Z
  file_id: '20229'
  file_name: 2025_Vorlaufer_Jakob_Thesis.pdf
  file_size: 10947446
  relation: main_file
  success: 1
file_date_updated: 2025-08-25T13:49:56Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20206
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '107'
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
  grant_number: CZI01
  name: CryoMinflux-guided in-situ molecular census and structure determination
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '19795'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
title: Construction of a cryo-super-resolution microscope to guide in situ structure
  analysis
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19003'
abstract:
- lang: eng
  text: 'Super-resolution methods provide far better spatial resolution than the optical
    diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
    they have yet to attain widespread use in plants, largely due to plants’ challenging
    optical properties. Expansion microscopy improves effective resolution by isotropically
    increasing the physical distances between sample structures while preserving relative
    spatial arrangements and clearing the sample. However, its application to plants
    has been hindered by the rigid, mechanically cohesive structure of plant tissues.
    Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
    thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
    conventional microscopy. Our results highlight the microtubule cytoskeleton organization
    and interaction between molecularly defined cellular constituents. Combining PlantEx
    with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
    and visualize the complex organization of subcellular organelles from intact tissues
    by example of the densely packed COPI-coated vesicles associated with the Golgi
    apparatus and put these into a cellular structural context. Our results show that
    expansion microscopy can be applied to increase effective imaging resolution in
    Arabidopsis root specimens. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: M-Shop
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
  at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
  workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis
  project has received funding from the European Research Council under the Horizon
  2020 Framework Programme (grant agreement No 742985, J.F.). It has also received
  funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie
  Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow
  from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement
  no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018).
  M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship
  no. 26137. The project has further received funding from the Austrian Science Fund,
  via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship
  from the Human Frontier Science Program (LT000557/2018). The funders had no role
  in study design, data collection and analysis, decision to publish or preparation
  of the manuscript."
article_number: koaf006
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Michelle C
  full_name: Gallei, Michelle C
  id: 35A03822-F248-11E8-B48F-1D18A9856A87
  last_name: Gallei
  orcid: 0000-0003-1286-7368
- first_name: Sven M
  full_name: Truckenbrodt, Sven M
  id: 45812BD4-F248-11E8-B48F-1D18A9856A87
  last_name: Truckenbrodt
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Syamala
  full_name: Inumella, Syamala
  id: F8660870-D756-11E9-98C5-34DFE5697425
  last_name: Inumella
  orcid: 0009-0002-5890-120X
- first_name: Vitali
  full_name: Vistunou, Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
- first_name: Wiebke
  full_name: Jahr, Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
  orcid: 0000-0003-0201-2315
- first_name: Marek
  full_name: Randuch, Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
- first_name: Alexander J
  full_name: Johnson, Alexander J
  id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
  last_name: Johnson
  orcid: 0000-0002-2739-8843
- first_name: Eva
  full_name: Benková, Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
    microscopy in plant roots. <i>The Plant Cell</i>. 2025;37(4). doi:<a href="https://doi.org/10.1093/plcell/koaf006">10.1093/plcell/koaf006</a>
  apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
    V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy
    in plant roots. <i>The Plant Cell</i>. Oxford University Press. <a href="https://doi.org/10.1093/plcell/koaf006">https://doi.org/10.1093/plcell/koaf006</a>
  chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
    Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
    Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>. Oxford University
    Press, 2025. <a href="https://doi.org/10.1093/plcell/koaf006">https://doi.org/10.1093/plcell/koaf006</a>.
  ieee: M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant
    roots,” <i>The Plant Cell</i>, vol. 37, no. 4. Oxford University Press, 2025.
  ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
    Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
    E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots.
    The Plant Cell. 37(4), koaf006.
  mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
    Roots.” <i>The Plant Cell</i>, vol. 37, no. 4, koaf006, Oxford University Press,
    2025, doi:<a href="https://doi.org/10.1093/plcell/koaf006">10.1093/plcell/koaf006</a>.
  short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
    C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
    A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).
corr_author: '1'
date_created: 2025-02-05T06:52:06Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-10-20T09:19:12Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1093/plcell/koaf006
ec_funded: 1
external_id:
  isi:
  - '001462763100001'
  pmid:
  - '39792900'
file:
- access_level: open_access
  checksum: 9d3f8218ff37a29f29c48a7bbe831bd3
  content_type: application/pdf
  creator: dernst
  date_created: 2025-07-31T07:03:43Z
  date_updated: 2025-07-31T07:03:43Z
  file_id: '20092'
  file_name: 2025_PlantCell_Gallei.pdf
  file_size: 53904111
  relation: main_file
  success: 1
file_date_updated: 2025-07-31T07:03:43Z
fulldoi: https://doi.org/10.1093/plcell/koaf006
has_accepted_license: '1'
intvolume: '        37'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
  grant_number: ALTF 679-2018
  name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
    X10 microscopy in combination with nanobodies and STED
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication: The Plant Cell
publication_identifier:
  eissn:
  - 1532-298X
  issn:
  - 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  record:
  - id: '18837'
    relation: research_data
    status: public
  - id: '18689'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Super-resolution expansion microscopy in plant roots
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2025'
...
---
OA_place: repository
_id: '18689'
abstract:
- lang: eng
  text: Multiplexed fluorescence microscopy imaging is widely used in biomedical applications.
    However, simultaneous imaging of multiple fluorophores can result in spectral
    leaks and overlapping, which greatly degrades image quality and subsequent analysis.
    Existing popular spectral unmixing methods are mainly based on computational intensive
    linear models and the performance is heavily dependent on the reference spectra,
    which may greatly preclude its further applications. In this paper, we propose
    a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate
    the physical spectral mixing process. A tranfer learning framework is further
    devised to allow our AutoUnmix adapting to a variety of imaging systems without
    retraining the network. Our proposed method has demonstrated real-time unmixing
    capabilities, surpassing existing methods by up to 100-fold in terms of unmixing
    speed. We further validate the reconstruction performance on both synthetic datasets
    and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM
    of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than
    other popular unmixing methods. Due to the desirable property of data independency
    and superior blind unmixing performance, we believe AutoUnmix is a powerful tool
    to study the interaction process of different organelles labeled by multiple fluorophores.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
  at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
  workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis
  project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D)
  and the European Research Council (ERC) under the European Union’s Horizon 2020
  research and innovation programme (grant agreement No 742985, J.F.). It has also
  received funding from the European Union’s Horizon 2020 research and innovation
  programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has
  received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research
  and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411
  and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further
  received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D.,
  J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral
  fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection
  and analysis, decision to publish or preparation of the manuscript."
article_processing_charge: No
author:
- first_name: Michelle C
  full_name: Gallei, Michelle C
  id: 35A03822-F248-11E8-B48F-1D18A9856A87
  last_name: Gallei
  orcid: 0000-0003-1286-7368
- first_name: Sven M
  full_name: Truckenbrodt, Sven M
  id: 45812BD4-F248-11E8-B48F-1D18A9856A87
  last_name: Truckenbrodt
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Syamala
  full_name: Inumella, Syamala
  id: F8660870-D756-11E9-98C5-34DFE5697425
  last_name: Inumella
  orcid: 0009-0002-5890-120X
- first_name: Vitali
  full_name: Vistunou, Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
- first_name: Wiebke
  full_name: Jahr, Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
  orcid: 0000-0003-0201-2315
- first_name: Marek
  full_name: Randuch, Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
- first_name: Alexander J
  full_name: Johnson, Alexander J
  id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
  last_name: Johnson
  orcid: 0000-0002-2739-8843
- first_name: Eva
  full_name: Benková, Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
    microscopy in plant roots. <i>bioRxiv</i>. doi:<a href="https://doi.org/10.1101/2024.02.21.581330">10.1101/2024.02.21.581330</a>
  apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
    V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy
    in plant roots. <i>bioRxiv</i>. <a href="https://doi.org/10.1101/2024.02.21.581330">https://doi.org/10.1101/2024.02.21.581330</a>
  chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
    Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
    Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2024.02.21.581330">https://doi.org/10.1101/2024.02.21.581330</a>.
  ieee: M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant
    roots,” <i>bioRxiv</i>. .
  ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
    Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
    E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv,
    <a href="https://doi.org/10.1101/2024.02.21.581330">10.1101/2024.02.21.581330</a>.
  mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
    Roots.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.1101/2024.02.21.581330">10.1101/2024.02.21.581330</a>.
  short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
    C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
    A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.02.21.581330
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2024.02.21.581330
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
  grant_number: ALTF 679-2018
  name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
    X10 microscopy in combination with nanobodies and STED
publication: bioRxiv
publication_status: draft
related_material:
  record:
  - id: '19003'
    relation: later_version
    status: public
  - id: '18681'
    relation: dissertation_contains
    status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: Super-resolution expansion microscopy in plant roots
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: preprint
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_embargo: '20'
OA_place: publisher
_id: '18681'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
citation:
  ama: 'Tavakoli M. Developing molecular and structural tools for studying brain architecture
    with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
    reconstruction with light microscopy. 2024. doi:<a href="https://doi.org/10.15479/at:ista:18681">10.15479/at:ista:18681</a>'
  apa: 'Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying
    brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
    connectomics reconstruction with light microscopy</i>. Institute of Science and
    Technology Austria. <a href="https://doi.org/10.15479/at:ista:18681">https://doi.org/10.15479/at:ista:18681</a>'
  chicago: 'Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying
    Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
    Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology
    Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18681">https://doi.org/10.15479/at:ista:18681</a>.'
  ieee: 'M. Tavakoli, “Developing molecular and structural tools for studying brain
    architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
    connectomics reconstruction with light microscopy,” Institute of Science and Technology
    Austria, 2024.'
  ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying
    brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
    connectomics reconstruction with light microscopy. Institute of Science and Technology
    Austria.'
  mla: 'Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying
    Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
    Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and
    Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:18681">10.15479/at:ista:18681</a>.'
  short: 'M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain
    Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
    Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology
    Austria, 2024.'
corr_author: '1'
das_tickbox: '1'
date_created: 2024-12-19T02:30:39Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '20'
ddc:
- '600'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18681
doi_confirm: '1'
file:
- access_level: closed
  checksum: b61651d417cafddd740a8528f46068c5
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: mtavakol
  date_created: 2024-12-20T10:23:17Z
  date_updated: 2024-12-20T10:31:37Z
  file_id: '18699'
  file_name: Thesis_Mojtaba Tavakoli_.docx
  file_size: 118593521
  relation: source_file
- access_level: closed
  checksum: c80bcfd1a34c23afc3538052325283e5
  content_type: application/pdf
  creator: mtavakol
  date_created: 2024-12-20T10:25:12Z
  date_updated: 2026-07-28T08:33:51Z
  embargo: 2027-08-01
  embargo_to: open_access
  file_id: '18700'
  file_name: Thesis_Mojtaba Tavakoli_.pdf
  file_size: 63885521
  relation: main_file
file_date_updated: 2026-07-28T08:33:51Z
fulldoi: https://doi.org/10.15479/at:ista:18681
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa_version: Published Version
page: '230'
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication_identifier:
  isbn:
  - 978-3-99078-048-0
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '11160'
    relation: part_of_dissertation
    status: public
  - id: '18688'
    relation: part_of_dissertation
    status: public
  - id: '18689'
    relation: part_of_dissertation
    status: public
  - id: '18677'
    relation: part_of_dissertation
    status: public
researchdata_availability: unclear
status: public
supervisor:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
supplementarymaterial: unclear
title: 'Developing molecular and structural tools for studying brain architecture
  with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
  reconstruction with light microscopy'
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
_id: '18677'
abstract:
- lang: eng
  text: The information-processing capability of the brain’s cellular network depends
    on the physical wiring pattern between neurons and their molecular and functional
    characteristics. Mapping neurons and resolving their individual synaptic connections
    can be achieved by volumetric imaging at nanoscale resolution with dense cellular
    labeling. Light microscopy is uniquely positioned to visualize specific molecules
    but dense, synapse-level circuit reconstruction by light microscopy has been out
    of reach due to limitations in resolution, contrast, and volumetric imaging capability.
    Here we developed light-microscopy based connectomics (LICONN). We integrated
    specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
    based segmentation and analysis of connectivity, thus directly incorporating molecular
    information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
    brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: E-Lib
- _id: M-Shop
- _id: LifeSc
- _id: Bio
- _id: ScienComp
acknowledgement: "We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript.
  We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics,
  Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and
  Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian
  Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC
  fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions
  Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
  (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
  Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n"
article_processing_charge: No
author:
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Michał
  full_name: Januszewski, Michał
  last_name: Januszewski
- first_name: Vitali
  full_name: Vistunou, Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Bárbara
  full_name: Oliveira, Bárbara
  id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
  last_name: Oliveira
- first_name: Alban
  full_name: Cenameri, Alban
  id: 9ac8f577-2357-11eb-997a-e566c5550886
  last_name: Cenameri
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Viren
  full_name: Jain, Viren
  last_name: Jain
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense
    connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href="https://doi.org/10.1101/2024.03.01.582884">10.1101/2024.03.01.582884</a>
  apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
    N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic
    reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href="https://doi.org/10.1101/2024.03.01.582884">https://doi.org/10.1101/2024.03.01.582884</a>
  chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
    Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy
    Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>,
    n.d. <a href="https://doi.org/10.1101/2024.03.01.582884">https://doi.org/10.1101/2024.03.01.582884</a>.
  ieee: M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction
    of mammalian brain tissue,” <i>bioRxiv</i>. .
  ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
    J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
    JG. Light-microscopy based dense connectomic reconstruction of mammalian brain
    tissue. bioRxiv, <a href="https://doi.org/10.1101/2024.03.01.582884">10.1101/2024.03.01.582884</a>.
  mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction
    of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.1101/2024.03.01.582884">10.1101/2024.03.01.582884</a>.
  short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
    J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
    V. Jain, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-18T14:48:24Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '08'
department:
- _id: GaNo
- _id: JoDa
doi: 10.1101/2024.03.01.582884
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.03.01.582884
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2024.03.01.582884
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
  grant_number: '101044865'
  name: Toward an understanding of the brain interstitial system and the extracellular
    proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
related_material:
  record:
  - id: '19704'
    relation: later_version
    status: public
  - id: '18674'
    relation: dissertation_contains
    status: public
  - id: '18681'
    relation: dissertation_contains
    status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: Light-microscopy based dense connectomic reconstruction of mammalian brain
  tissue
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: preprint
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
_id: '18688'
abstract:
- lang: eng
  text: The human brain has remarkable computational power. It generates sophisticated
    behavioral sequences, stores engrams over an individual’s lifetime, and produces
    higher cognitive functions up to the level of consciousness. However, so little
    of our neuroscience knowledge covers the human brain, and it remains unknown whether
    this organ is truly unique, or is a scaled version of the extensively studied
    rodent brain. To address this fundamental question, we determined the cellular,
    synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using
    multicellular patch clamp-recording. This circuit is the largest autoassociative
    network in the brain, and plays a key role in memory and higher-order computations
    such as pattern separation and pattern completion. We demonstrate that human hippocampal
    CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks.
    Connectivity sparsifies from rodents to humans, providing a circuit architecture
    that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses
    showed both distinct species-specific and circuit-dependent properties, with high
    reliability, unique amplitude precision, and long integration times. We also identify
    differential scaling rules between hippocampal pathways from rodents to humans,
    with a moderate increase in the convergence of CA3 inputs per cell, but a marked
    increase in human mossy fiber innervation. Anatomically guided full-scale modeling
    suggests that the human brain’s sparse connectivity, expanded neuronal number,
    and reliable synaptic signaling combine to enhance the associative memory storage
    capacity of CA3. Together, our results reveal unique rules of connectivity and
    synaptic signaling in the human hippocampus, demonstrating the absolute necessity
    of human brain research and beginning to unravel the remarkable performance of
    our autoassociative memory circuits.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: PreCl
- _id: ScienComp
acknowledgement: We thank Florian Marr for excellent technical assistance, Christina
  Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor
  Asenov for development of the transportation box for human brain tissue, Tim Vogels
  for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria
  Kralli-Beller for manuscript editing. This research was supported by the Scientific
  Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from
  Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life
  Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge
  the excellent support of the Medical University of Vienna Department of Neurosurgery
  staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry,
  and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology.
  The project received funding from the European Research Council (ERC) under the
  European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie
  Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund
  (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian
  Academy of Sciences (DOC fellowship 26137 to M.R.T.).
article_processing_charge: No
author:
- first_name: Jake F.
  full_name: Watson, Jake F.
  last_name: Watson
- first_name: Victor
  full_name: Vargas-Barroso, Victor
  last_name: Vargas-Barroso
- first_name: Rebecca J.
  full_name: Morse-Mora, Rebecca J.
  last_name: Morse-Mora
- first_name: Andrea
  full_name: Navas-Olive, Andrea
  last_name: Navas-Olive
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Matthias
  full_name: Tomschik, Matthias
  last_name: Tomschik
- first_name: Karl
  full_name: Rössler, Karl
  last_name: Rössler
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
citation:
  ama: Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses
    specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>.
    doi:<a href="https://doi.org/10.1101/2024.05.02.592169">10.1101/2024.05.02.592169</a>
  apa: Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli,
    M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional
    connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href="https://doi.org/10.1101/2024.05.02.592169">https://doi.org/10.1101/2024.05.02.592169</a>
  chicago: Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive,
    Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M
    Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for
    Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2024.05.02.592169">https://doi.org/10.1101/2024.05.02.592169</a>.
  ieee: J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional
    connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .
  ista: Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl
    JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional
    connectivity rules for efficient associative memory. bioRxiv, <a href="https://doi.org/10.1101/2024.05.02.592169">10.1101/2024.05.02.592169</a>.
  mla: Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity
    Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.1101/2024.05.02.592169">10.1101/2024.05.02.592169</a>.
  short: J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli,
    J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T11:35:08Z
date_published: 2024-05-02T00:00:00Z
date_updated: 2026-10-20T08:20:04Z
day: '02'
department:
- _id: JoDa
- _id: PeJo
doi: 10.1101/2024.05.02.592169
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.05.02.592169
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2024.05.02.592169
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
  call_identifier: H2020
  grant_number: '101026635'
  name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
publication: bioRxiv
publication_status: draft
related_material:
  record:
  - id: '18681'
    relation: dissertation_contains
    status: public
  - id: '18879'
    relation: later_version
    status: public
status: public
title: Human hippocampal CA3 uses specific functional connectivity rules for efficient
  associative memory
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '14257'
abstract:
- lang: eng
  text: Mapping the complex and dense arrangement of cells and their connectivity
    in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
    optical microscopy excels at visualizing specific molecules and individual cells
    but fails to provide tissue context. Here we developed Comprehensive Analysis
    of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
    from millimeter regional to nanometer synaptic scales in diverse chemically fixed
    brain preparations, including rodent and human. CATS uses fixation-compatible
    extracellular labeling and optical imaging, including stimulated emission depletion
    or expansion microscopy, to comprehensively delineate cellular structures. It
    enables three-dimensional reconstruction of single synapses and mapping of synaptic
    connectivity by identification and analysis of putative synaptic cleft regions.
    Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
    and quantified the synaptic input and output structure of identified neurons.
    We furthermore demonstrate applicability to clinically derived human tissue samples,
    including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
    the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
  for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
  Erber for technical assistance; and M. Tomschik for support with obtaining human
  samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
  for computational support and hardware control. We are grateful to R. Shigemoto
  and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
  for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
  provided by S. Grant (University of Edinburgh). We acknowledge expert support by
  Institute of Science and Technology Austria’s scientific computing, imaging and
  optics, preclinical and lab support facilities and by the Miba machine shop and
  library. We gratefully acknowledge funding by the following sources: Austrian Science
  Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
  (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
  (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
  (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
  European Union’s Horizon 2020 research and innovation programme, European Research
  Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
  research and innovation programme, European Research Council (ERC) grant 692692
  – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
  the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
  Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
  full_name: Michalska, Julia M
  id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
  last_name: Michalska
  orcid: 0000-0003-3862-1235
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Philipp
  full_name: Velicky, Philipp
  id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
  last_name: Velicky
  orcid: 0000-0002-2340-7431
- first_name: Hana
  full_name: Korinkova, Hana
  id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
  last_name: Korinkova
- first_name: Jake
  full_name: Watson, Jake
  id: 63836096-4690-11EA-BD4E-32803DDC885E
  last_name: Watson
  orcid: 0000-0002-8698-3823
- first_name: Alban
  full_name: Cenameri, Alban
  id: 9ac8f577-2357-11eb-997a-e566c5550886
  last_name: Cenameri
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Nicole
  full_name: Amberg, Nicole
  id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
  last_name: Amberg
  orcid: 0000-0002-3183-8207
- first_name: Alessandro
  full_name: Venturino, Alessandro
  id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
  last_name: Venturino
  orcid: 0000-0003-2356-9403
- first_name: Karl
  full_name: Roessler, Karl
  last_name: Roessler
- first_name: Thomas
  full_name: Czech, Thomas
  last_name: Czech
- first_name: Romana
  full_name: Höftberger, Romana
  last_name: Höftberger
- first_name: Sandra
  full_name: Siegert, Sandra
  id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
  last_name: Siegert
  orcid: 0000-0001-8635-0877
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
    across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064.
    doi:<a href="https://doi.org/10.1038/s41587-023-01911-8">10.1038/s41587-023-01911-8</a>
  apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
    A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter
    to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href="https://doi.org/10.1038/s41587-023-01911-8">https://doi.org/10.1038/s41587-023-01911-8</a>
  chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
    Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
    across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer
    Nature, 2024. <a href="https://doi.org/10.1038/s41587-023-01911-8">https://doi.org/10.1038/s41587-023-01911-8</a>.
  ieee: J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter
    to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp.
    1051–1064, 2024.
  ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
    CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
    G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter
    to nanometer scales. Nature Biotechnology. 42, 1051–1064.
  mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
    to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024,
    pp. 1051–64, doi:<a href="https://doi.org/10.1038/s41587-023-01911-8">10.1038/s41587-023-01911-8</a>.
  short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
    C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
    Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.
corr_author: '1'
das_tickbox: '1'
date_created: 2023-09-03T22:01:15Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-21T08:36:20Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
  isi:
  - '001065254200001'
  pmid:
  - '37653226'
file:
- access_level: open_access
  checksum: 57d5fafb16f02dcb9f7dddb1bd7e2a71
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-09T07:48:01Z
  date_updated: 2025-01-09T07:48:01Z
  file_id: '18784'
  file_name: 2024_NatureBiotech_Michalska.pdf
  file_size: 26065165
  relation: main_file
  success: 1
file_date_updated: 2025-01-09T07:48:01Z
fulldoi: https://doi.org/10.1038/s41587-023-01911-8
has_accepted_license: '1'
intvolume: '        42'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1051-1064
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I03600
  name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00312
  name: Synaptic communication in neuronal microcircuits
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
  grant_number: LS18-022
  name: High content imaging to decode human immune cell interactions in health and
    allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715508'
  name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
    and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '692692'
  name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
  call_identifier: H2020
  grant_number: '101026635'
  name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
  eissn:
  - 1546-1696
  issn:
  - 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/danzllab/CATS
  record:
  - id: '18660'
    relation: dissertation_contains
    status: deleted
  - id: '13126'
    relation: research_data
    status: public
  - id: '18674'
    relation: dissertation_contains
    status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Imaging brain tissue architecture across millimeter to nanometer scales
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
year: '2024'
...
---
OA_place: publisher
_id: '18674'
abstract:
- lang: eng
  text: Mapping the complex and dense arrangement of cells and their connectivity
    in brain tissue requires volumetric imaging at nanoscale spatial resolution. While
    light microscopy excels at visualizing specific molecules and individual cells,
    achieving dense, synapse-level circuit reconstruction has not been possible with
    any light microscopy technique. Thus, the goal of my work was to develop image
    and data analysis pipelines for brain tissue visualization and reconstruction
    with light microscopy. To achieve dense circuit reconstruction with single-synapse
    resolution, I developed both conventional and deep-learning-based synapse detection
    algorithms, as well as connectivity analysis pipelines that integrate synapse
    detection with volumetric segmentation of brain tissue.
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
citation:
  ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution
    light microscopy. 2024. doi:<a href="https://doi.org/10.15479/at:ista:18674">10.15479/at:ista:18674</a>
  apa: Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with
    super-resolution light microscopy</i>. Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/at:ista:18674">https://doi.org/10.15479/at:ista:18674</a>
  chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution
    Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18674">https://doi.org/10.15479/at:ista:18674</a>.
  ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution
    light microscopy,” Institute of Science and Technology Austria, 2024.
  ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution
    light microscopy. Institute of Science and Technology Austria.
  mla: Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution
    Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a
    href="https://doi.org/10.15479/at:ista:18674">10.15479/at:ista:18674</a>.
  short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution
    Light Microscopy, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-18T14:24:43Z
date_published: 2024-12-18T00:00:00Z
date_updated: 2026-10-21T08:36:19Z
day: '18'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18674
doi_confirm: '1'
ec_funded: 1
file:
- access_level: open_access
  checksum: 1b42b8073e2bc09fc504da52372248c1
  content_type: application/pdf
  creator: jlyudchi
  date_created: 2024-12-18T14:17:34Z
  date_updated: 2024-12-18T14:17:34Z
  file_id: '18675'
  file_name: 18122024_PhDthesis_corrected_final_pdfa.pdf
  file_size: 160536833
  relation: main_file
  success: 1
- access_level: closed
  checksum: b4da84624060745519723698f7ddf54b
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: jlyudchi
  date_created: 2024-12-18T14:21:06Z
  date_updated: 2024-12-18T14:41:53Z
  file_id: '18676'
  file_name: 18122024_PhDthesis_corrected_final_JL_markup.docx
  file_size: 99172203
  relation: source_file
file_date_updated: 2024-12-18T14:41:53Z
fulldoi: https://doi.org/10.15479/at:ista:18674
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '217'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication_identifier:
  isbn:
  - ' 978-3-99078-051-0'
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '11160'
    relation: part_of_dissertation
    status: public
  - id: '13267'
    relation: part_of_dissertation
    status: public
  - id: '18677'
    relation: part_of_dissertation
    status: public
  - id: '14257'
    relation: part_of_dissertation
    status: public
researchdata_availability: no
status: public
supervisor:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
supplementarymaterial: no
title: Image analysis for brain tissue reconstruction with super-resolution light
  microscopy
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
_id: '18471'
abstract:
- lang: eng
  text: "Spatial omics technologies are enriching our understanding of complex biological
    samples, by\r\nallowing us to study their molecular composition while preserving
    the spatial relationships\r\nbetween molecules in their native context. As the
    field continues to advance, there are\r\ntechnical challenges that need to be
    addressed in order to take full advantage of the spatial\r\ncapabilities of these
    methods. In this work, I present two technical developments that I\r\nestablished
    for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial
    resolution limits to the nanoscale, and (2) adding rich tissue context to the
    mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in
    cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and
    expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm,
    and explored the compatibility of MERFISH with singlemolecule localization microscopy
    (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied
    the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides
    an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully
    established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse
    brain slices, being able to extract transcriptomics information with 3D tissue
    context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize
    the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding
    light on the neuropil-specific\r\ntranscriptome. This method provides integrated
    information on cellular structure and\r\ntranscriptomes in situ, and could potentially
    be applied with other modalities, opening new\r\navenues for scientific discovery. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
citation:
  ama: Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue
    context. 2024. doi:<a href="https://doi.org/10.15479/at:ista:18471">10.15479/at:ista:18471</a>
  apa: Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape
    with tissue context</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:18471">https://doi.org/10.15479/at:ista:18471</a>
  chicago: Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape
    with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18471">https://doi.org/10.15479/at:ista:18471</a>.
  ieee: N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with
    tissue context,” Institute of Science and Technology Austria, 2024.
  ista: Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape
    with tissue context. Institute of Science and Technology Austria.
  mla: Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape
    with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a
    href="https://doi.org/10.15479/at:ista:18471">10.15479/at:ista:18471</a>.
  short: N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with
    Tissue Context, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-26T20:02:42Z
date_published: 2024-10-28T00:00:00Z
date_updated: 2026-10-02T11:26:48Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18471
doi_confirm: '1'
ec_funded: 1
file:
- access_level: closed
  checksum: 6d7c7725d040d8debc070dcb35ac965d
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: nagudelo
  date_created: 2024-10-26T22:29:06Z
  date_updated: 2025-05-05T22:30:04Z
  embargo_to: open_access
  file_id: '18475'
  file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx
  file_size: 183077763
  relation: source_file
- access_level: open_access
  checksum: 52f9c0bf2bdafa3baf827b73814a53ff
  content_type: application/pdf
  creator: nagudelo
  date_created: 2024-10-26T23:13:33Z
  date_updated: 2025-05-05T22:30:04Z
  embargo: 2025-05-05
  file_id: '18476'
  file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf
  file_size: 47027710
  relation: main_file
file_date_updated: 2025-05-05T22:30:04Z
fulldoi: https://doi.org/10.15479/at:ista:18471
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '97'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
publication_identifier:
  isbn:
  - 978-3-99078-044-2
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
researchdata_availability: unclear
status: public
supervisor:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
supplementarymaterial: unclear
title: Visualizing the neuronal transcriptional landscape with tissue context
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '12115'
acknowledgement: This work was supported by European Commission’s Seventh Framework
  Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
  full_name: Glajzer, Jacek
  last_name: Glajzer
- first_name: Dan Cacsire
  full_name: Castillo-Tong, Dan Cacsire
  last_name: Castillo-Tong
- first_name: Rolf
  full_name: Richter, Rolf
  last_name: Richter
- first_name: Ignace
  full_name: Vergote, Ignace
  last_name: Vergote
- first_name: Hagen
  full_name: Kulbe, Hagen
  last_name: Kulbe
- first_name: Adriaan
  full_name: Vanderstichele, Adriaan
  last_name: Vanderstichele
- first_name: Ilary
  full_name: Ruscito, Ilary
  last_name: Ruscito
- first_name: Fabian
  full_name: Trillsch, Fabian
  last_name: Trillsch
- first_name: Alexander
  full_name: Mustea, Alexander
  last_name: Mustea
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Charlie
  full_name: Gourley, Charlie
  last_name: Gourley
- first_name: Hani
  full_name: Gabra, Hani
  last_name: Gabra
- first_name: Eliane T.
  full_name: Taube, Eliane T.
  last_name: Taube
- first_name: Oliver
  full_name: Dorigo, Oliver
  last_name: Dorigo
- first_name: David
  full_name: Horst, David
  last_name: Horst
- first_name: Carlotta
  full_name: Keunecke, Carlotta
  last_name: Keunecke
- first_name: Joanna
  full_name: Baum, Joanna
  last_name: Baum
- first_name: Timothy
  full_name: Angelotti, Timothy
  last_name: Angelotti
- first_name: Jalid
  full_name: Sehouli, Jalid
  last_name: Sehouli
- first_name: Elena Ioana
  full_name: Braicu, Elena Ioana
  last_name: Braicu
citation:
  ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact
    of BRCA mutation status on tumor dissemination pattern, surgical outcome, and
    patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC).
    A multicenter, retrospective study of the ovarian cancer therapy—innovative models
    prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. 2023;30:46-47.
    doi:<a href="https://doi.org/10.1245/s10434-022-12681-z">10.1245/s10434-022-12681-z</a>'
  apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
    A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status
    on tumor dissemination pattern, surgical outcome, and patient survival in primary
    and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
    study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
    consortium. <i>Annals of Surgical Oncology</i>. Springer Nature. <a href="https://doi.org/10.1245/s10434-022-12681-z">https://doi.org/10.1245/s10434-022-12681-z</a>'
  chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
    Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract:
    Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome,
    and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer
    (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative
    Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>.
    Springer Nature, 2023. <a href="https://doi.org/10.1245/s10434-022-12681-z">https://doi.org/10.1245/s10434-022-12681-z</a>.'
  ieee: 'J. Glajzer <i>et al.</i>, “ASO Visual Abstract: Impact of BRCA mutation status
    on tumor dissemination pattern, surgical outcome, and patient survival in primary
    and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
    study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
    consortium,” <i>Annals of Surgical Oncology</i>, vol. 30. Springer Nature, pp.
    46–47, 2023.'
  ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
    A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
    Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
    ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern,
    surgical outcome, and patient survival in primary and recurrent high-grade serous
    ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer
    therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical
    Oncology. 30, 46–47.'
  mla: 'Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status
    on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary
    and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective
    Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS)
    Consortium.” <i>Annals of Surgical Oncology</i>, vol. 30, Springer Nature, 2023,
    pp. 46–47, doi:<a href="https://doi.org/10.1245/s10434-022-12681-z">10.1245/s10434-022-12681-z</a>.'
  short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
    I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
    Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
    Braicu, Annals of Surgical Oncology 30 (2023) 46–47.
date_created: 2023-01-12T11:56:22Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2026-06-18T17:21:25Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12681-z
external_id:
  isi:
  - '000879151800001'
fulldoi: https://doi.org/10.1245/s10434-022-12681-z
intvolume: '        30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1245/s10434-022-12681-z
month: '01'
oa: 1
oa_version: Published Version
page: 46-47
publication: Annals of Surgical Oncology
publication_identifier:
  eissn:
  - 1534-4681
  issn:
  - 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '12205'
    relation: other
    status: public
scopus_import: '1'
status: public
title: 'ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination
  pattern, surgical outcome, and patient survival in primary and recurrent high-grade
  serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian
  cancer therapy—innovative models prolong survival (OCTIPS) consortium'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '12205'
abstract:
- lang: eng
  text: "Background: This study seeks to evaluate the impact of breast cancer (BRCA)
    gene status on tumor dissemination pattern, surgical outcome and survival in a
    multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian
    cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data
    from 190 patients were gathered retrospectively. All patients had surgery at pOC
    and at least one further rOC surgery at four European high-volume centers. Patients
    were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut)
    and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor
    presentation, surgical outcome and survival data were analyzed between the two
    groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years
    younger and had significantly more tumor involvement upon diagnosis. Patients
    with BRCAmut disease showed higher debulking rates at all stages. Multivariate
    analysis showed that only patient age had significant predictive value for complete
    tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated
    with optimal debulking. Patients with BRCAmut disease showed significantly prolonged
    overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged
    in the BRCAmut group at all stages as well, reaching statistical significance
    during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a
    more aggressive course of disease with earlier onset and more extensive tumor
    dissemination at pOC. However, surgical outcome and OS were significantly better
    in patients with BRCAmut disease compared with patients with BRCAwt disease. We
    therefore propose to consider BRCAmut status in regard to patient selection for
    cytoreductive surgery, especially in rOC."
acknowledgement: "E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a
  participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin
  Berlin and the Berlin Institute of Health. This work was supported by European Commission’s
  Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen
  Access funding enabled and organized by Projekt DEAL."
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
  full_name: Glajzer, Jacek
  last_name: Glajzer
- first_name: Dan Cacsire
  full_name: Castillo-Tong, Dan Cacsire
  last_name: Castillo-Tong
- first_name: Rolf
  full_name: Richter, Rolf
  last_name: Richter
- first_name: Ignace
  full_name: Vergote, Ignace
  last_name: Vergote
- first_name: Hagen
  full_name: Kulbe, Hagen
  last_name: Kulbe
- first_name: Adriaan
  full_name: Vanderstichele, Adriaan
  last_name: Vanderstichele
- first_name: Ilary
  full_name: Ruscito, Ilary
  last_name: Ruscito
- first_name: Fabian
  full_name: Trillsch, Fabian
  last_name: Trillsch
- first_name: Alexander
  full_name: Mustea, Alexander
  last_name: Mustea
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Charlie
  full_name: Gourley, Charlie
  last_name: Gourley
- first_name: Hani
  full_name: Gabra, Hani
  last_name: Gabra
- first_name: Eliane T.
  full_name: Taube, Eliane T.
  last_name: Taube
- first_name: Oliver
  full_name: Dorigo, Oliver
  last_name: Dorigo
- first_name: David
  full_name: Horst, David
  last_name: Horst
- first_name: Carlotta
  full_name: Keunecke, Carlotta
  last_name: Keunecke
- first_name: Joanna
  full_name: Baum, Joanna
  last_name: Baum
- first_name: Timothy
  full_name: Angelotti, Timothy
  last_name: Angelotti
- first_name: Jalid
  full_name: Sehouli, Jalid
  last_name: Sehouli
- first_name: Elena Ioana
  full_name: Braicu, Elena Ioana
  last_name: Braicu
citation:
  ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status
    on tumor dissemination pattern, surgical outcome and patient survival in primary
    and recurrent high-grade serous ovarian cancer: A multicenter retrospective study
    by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium.
    <i>Annals of Surgical Oncology</i>. 2023;30:35-45. doi:<a href="https://doi.org/10.1245/s10434-022-12459-3">10.1245/s10434-022-12459-3</a>'
  apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
    A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination
    pattern, surgical outcome and patient survival in primary and recurrent high-grade
    serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
    Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. <i>Annals of Surgical
    Oncology</i>. Springer Nature. <a href="https://doi.org/10.1245/s10434-022-12459-3">https://doi.org/10.1245/s10434-022-12459-3</a>'
  chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
    Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation
    Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in
    Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective
    Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.”
    <i>Annals of Surgical Oncology</i>. Springer Nature, 2023. <a href="https://doi.org/10.1245/s10434-022-12459-3">https://doi.org/10.1245/s10434-022-12459-3</a>.'
  ieee: 'J. Glajzer <i>et al.</i>, “Impact of BRCA mutation status on tumor dissemination
    pattern, surgical outcome and patient survival in primary and recurrent high-grade
    serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
    Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” <i>Annals of
    Surgical Oncology</i>, vol. 30. Springer Nature, pp. 35–45, 2023.'
  ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
    A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
    Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
    Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
    and patient survival in primary and recurrent high-grade serous ovarian cancer:
    A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
    Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.'
  mla: 'Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination
    Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade
    Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer
    Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of
    Surgical Oncology</i>, vol. 30, Springer Nature, 2023, pp. 35–45, doi:<a href="https://doi.org/10.1245/s10434-022-12459-3">10.1245/s10434-022-12459-3</a>.'
  short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
    I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
    Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
    Braicu, Annals of Surgical Oncology 30 (2023) 35–45.
date_created: 2023-01-16T09:44:36Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2026-06-18T17:21:24Z
day: '01'
ddc:
- '610'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12459-3
external_id:
  isi:
  - '000852125500006'
  pmid:
  - '36085390'
file:
- access_level: open_access
  checksum: 36a1200e1011f4b2155a8041d0308f34
  content_type: application/pdf
  creator: dernst
  date_created: 2023-02-02T13:01:20Z
  date_updated: 2023-02-02T13:01:20Z
  file_id: '12490'
  file_name: 2023_AnnalsSurgicalOncology_Glajzer.pdf
  file_size: 365865
  relation: main_file
  success: 1
file_date_updated: 2023-02-02T13:01:20Z
fulldoi: https://doi.org/10.1245/s10434-022-12459-3
has_accepted_license: '1'
intvolume: '        30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 35-45
pmid: 1
publication: Annals of Surgical Oncology
publication_identifier:
  eissn:
  - 1534-4681
  issn:
  - 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '12115'
    relation: other
    status: public
scopus_import: '1'
status: public
title: 'Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
  and patient survival in primary and recurrent high-grade serous ovarian cancer:
  A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
  Prolong Survival (OCTIPS) consortium'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '12817'
abstract:
- lang: eng
  text: 3D-reconstruction of living brain tissue down to individual synapse level
    would create opportunities for decoding the dynamics and structure-function relationships
    of the brain’s complex and dense information processing network. However, it has
    been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio,
    and prohibitive light burden in optical imaging, whereas electron microscopy is
    inherently static. Here we solved these challenges by developing an integrated
    optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy
    Enabling Saturated Segmentation). It leverages optical modifications to stimulated
    emission depletion (STED) microscopy in comprehensively, extracellularly labelled
    tissue and prior information on sample structure via machine learning to simultaneously
    achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility
    with living tissue. This allows dense deep-learning-based instance segmentation
    and 3D-reconstruction at synapse level incorporating molecular, activity, and
    morphodynamic information. LIONESS opens up avenues for studying the dynamic functional
    (nano-)architecture of living brain tissue.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance
  and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and
  M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial
  exploration of software. We thank Paul Henderson for advice on deep-learning training
  and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading
  of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag
  ligand. '
article_processing_charge: No
author:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction
    of living brain tissue.” 2023. doi:<a href="https://doi.org/10.15479/AT:ISTA:12817">10.15479/AT:ISTA:12817</a>
  apa: Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale
    reconstruction of living brain tissue.” Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/AT:ISTA:12817">https://doi.org/10.15479/AT:ISTA:12817</a>
  chicago: Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale
    Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria,
    2023. <a href="https://doi.org/10.15479/AT:ISTA:12817">https://doi.org/10.15479/AT:ISTA:12817</a>.
  ieee: J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction
    of living brain tissue.’” Institute of Science and Technology Austria, 2023.
  ista: Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction
    of living brain tissue’, Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:12817">10.15479/AT:ISTA:12817</a>.
  mla: Danzl, Johann G. <i>Research Data for the Publication “Dense 4D Nanoscale Reconstruction
    of Living Brain Tissue.”</i> Institute of Science and Technology Austria, 2023,
    doi:<a href="https://doi.org/10.15479/AT:ISTA:12817">10.15479/AT:ISTA:12817</a>.
  short: J.G. Danzl, (2023).
contributor:
- first_name: Philipp
  id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
  last_name: Velicky
  orcid: 0000-0002-2340-7431
- first_name: Eder
  id: 3FB91342-F248-11E8-B48F-1D18A9856A87
  last_name: Miguel Villalba
- first_name: Julia M
  id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
  last_name: Michalska
- first_name: Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Donglai
  last_name: Wei
- first_name: Zudi
  last_name: Lin
- first_name: Jake
  id: 63836096-4690-11EA-BD4E-32803DDC885E
  last_name: Watson
  orcid: 0000-0002-8698-3823
- first_name: Jakob
  last_name: Troidl
- first_name: Johanna
  last_name: Beyer
- first_name: Yoav
  id: 43DF3136-F248-11E8-B48F-1D18A9856A87
  last_name: Ben Simon
- first_name: Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
- first_name: Alban
  id: 9ac8f577-2357-11eb-997a-e566c5550886
  last_name: Cenameri
- first_name: Johannes
  last_name: Broichhagen
- first_name: 'Seth G. N. '
  last_name: Grant
- first_name: Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
- first_name: Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Hanspeter
  last_name: Pfister
- first_name: Bernd
  id: 49876194-F248-11E8-B48F-1D18A9856A87
  last_name: Bickel
  orcid: 0000-0001-6511-9385
corr_author: '1'
date_created: 2023-04-07T11:37:40Z
date_published: 2023-05-19T00:00:00Z
date_updated: 2026-04-14T08:34:34Z
day: '19'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.15479/AT:ISTA:12817
file:
- access_level: open_access
  checksum: c1819889e72ec86ee1bba809e19739e0
  content_type: text/plain
  creator: jdanzl
  date_created: 2023-05-18T17:06:12Z
  date_updated: 2023-05-18T17:06:12Z
  file_id: '13030'
  file_name: Readme.txt
  file_size: 651
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8f6259fc5128ffcc0cd89d25d51995c1
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T19:51:52Z
  date_updated: 2023-05-18T19:51:52Z
  file_id: '13031'
  file_name: Fig1a_LIONESS.tif
  file_size: 347448884
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 204e8ef763b5a122fa95a594f5217d83
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:48:26Z
  date_updated: 2023-05-18T16:48:26Z
  file_id: '13029'
  file_name: Fig_1b.tif
  file_size: 91626
  relation: main_file
  success: 1
- access_level: open_access
  checksum: dc521a4e6e80a57c100a06ba1e87c766
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:48:26Z
  date_updated: 2023-05-18T16:48:26Z
  file_id: '13028'
  file_name: Fig_1c.tif
  file_size: 90300
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 56d3d5dbe7e1f54dbecc32ad2d2cc6df
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:00:06Z
  date_updated: 2023-05-18T16:00:06Z
  file_id: '13022'
  file_name: Figure2a_low_exposure_input.tif
  file_size: 18391928
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 2c30dbd6c4db079f7fdc2eaeea5f9710
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:59:30Z
  date_updated: 2023-05-18T15:59:30Z
  file_id: '13021'
  file_name: Figure2a_LIONESS.tif
  file_size: 18392017
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 799868024bf734fecaf36f4ffd843ed2
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:58:54Z
  date_updated: 2023-05-18T15:58:54Z
  file_id: '13020'
  file_name: Figure2a_merge_LIONESS_EGFP.tif
  file_size: 36785440
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 522fe0fe505e437d6f637f9b8059dfaa
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:44:45Z
  date_updated: 2023-05-18T16:44:45Z
  file_id: '13025'
  file_name: Fig2c_LIONESS.tif
  file_size: 670051576
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c9c0d873341d2f974ba799fa71a1b789
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:23:10Z
  date_updated: 2023-05-18T16:23:10Z
  file_id: '13024'
  file_name: Fig2de_LIONESS_1.tif
  file_size: 412478217
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ff86ad8642c56ba1c67c814e20925a85
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T19:48:02Z
  date_updated: 2023-05-18T19:48:02Z
  file_id: '13032'
  file_name: Fig2de_LIONESS_2.tif
  file_size: 637360217
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 32681bd33673088193fad9f9c7b79090
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:39:05Z
  date_updated: 2023-05-18T14:39:05Z
  file_id: '12995'
  file_name: Fig_3_LIONESS.zip
  file_size: 46563159
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 17239ed0f54ac7495e2b1daa5d0864ef
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:04:40Z
  date_updated: 2023-05-18T15:04:40Z
  file_id: '13001'
  file_name: Fig_4_LIONESS_synaptic_markers.zip
  file_size: 29159397
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c060c898f2bf93312a4c07dfdcb745cb
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:58:09Z
  date_updated: 2023-05-18T14:58:09Z
  file_id: '12997'
  file_name: Fig_5a_time_series_Ca2+_imaging.zip
  file_size: 16563855
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 85b4c0cd099212ecf0beec3a78bb35c5
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:55:44Z
  date_updated: 2023-05-18T15:55:44Z
  file_id: '13017'
  file_name: Fig5b_LIONESS_T1.tif
  file_size: 30632526
  relation: main_file
  success: 1
- access_level: open_access
  checksum: eb83649a0ebc2f5ea7a0308324ebf308
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:57:40Z
  date_updated: 2023-05-18T15:57:40Z
  file_id: '13018'
  file_name: Fig5b_LIONESS_T2.tif
  file_size: 57634426
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 40a2d93a34f83ce37043d8414d981b3d
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:14:33Z
  date_updated: 2023-05-18T15:14:33Z
  file_id: '13005'
  file_name: Extended_Data_Figure 3a_low_exposure.tif
  file_size: 12512676
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 516521bb400f5c058184994b57165f8b
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:15:01Z
  date_updated: 2023-05-18T15:15:01Z
  file_id: '13006'
  file_name: Extended_Data_Figure 3a_high_exposure.tif
  file_size: 12512678
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1d3a21970307de2d84b614985ec0706d
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:17:08Z
  date_updated: 2023-05-18T15:17:08Z
  file_id: '13007'
  file_name: Extended_Data_Figure 3a_restored.tif
  file_size: 50038242
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 441575853bf667ed89cc218079cc397b
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:56:57Z
  date_updated: 2023-05-18T15:56:57Z
  file_id: '13016'
  file_name: Extended_Data_Figure 3b_example dataset_low_exposure_input.tif
  file_size: 68298045
  relation: main_file
  success: 1
- access_level: open_access
  checksum: e499355760270e14bcf12bdc7960bd7a
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:54:43Z
  date_updated: 2023-05-18T15:54:43Z
  file_id: '13015'
  file_name: Extended_Data_Figure 3b_example dataset_merge_LIONESS_EGFP.tif
  file_size: 136597524
  relation: main_file
  success: 1
- access_level: open_access
  checksum: add9f1adc6763091233dbe8504f1c396
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:50:19Z
  date_updated: 2023-05-18T15:50:19Z
  file_id: '13014'
  file_name: Extended_Data_Figure 3b_dataset_1_merge_LIONESS_EGFP.tif
  file_size: 76103800
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 311719efb1c68d7243be557b779173f2
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:51:20Z
  date_updated: 2023-05-18T15:51:20Z
  file_id: '13013'
  file_name: Extended_Data_Figure 3b_dataset_2_merge_LIONESS_EGFP.tif
  file_size: 49810007
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8d5d9d859f8d099bb3b877c4e455f699
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:32:55Z
  date_updated: 2023-05-18T15:32:55Z
  file_id: '13010'
  file_name: Extended_Data_Figure 3b_dataset_3_merge_LIONESS_EGFP.tif
  file_size: 169060658
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 79eca23cc5e2fc1fe26e03e1bba2e90f
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:47:03Z
  date_updated: 2023-05-18T15:47:03Z
  file_id: '13011'
  file_name: Extended_Data_Figure 3b_dataset_4_merge_LIONESS_EGFP.tif
  file_size: 169060658
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 107bf2e0f8a14b4bd0169c9104765171
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:47:47Z
  date_updated: 2023-05-18T15:47:47Z
  file_id: '13012'
  file_name: Extended_Data_Figure 3b_dataset_5_merge_LIONESS_EGFP.tif
  file_size: 244861000
  relation: main_file
  success: 1
- access_level: open_access
  checksum: b71e4a090dd9a8048aee847ae47624f0
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:36:34Z
  date_updated: 2023-05-18T14:36:34Z
  file_id: '12994'
  file_name: Extended_Data_Fig_4_LIONESS_TIF_stacks.zip
  file_size: 76795968
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ea011c3d1966ba79a62e8cf775e595c5
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:09:31Z
  date_updated: 2023-05-18T16:09:31Z
  file_id: '13023'
  file_name: Extended_Data_Fig5b.tif
  file_size: 288330201
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1c56b5b324b6270b0df72a77e1e9d6f1
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:21:29Z
  date_updated: 2023-05-18T15:21:29Z
  file_id: '13003'
  file_name: Extended_Data_Fig_6_TIF_stacks.zip
  file_size: 255976297
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 89150ebb0044ead282b9048e55cd3961
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:08:20Z
  date_updated: 2023-05-18T15:08:20Z
  file_id: '13002'
  file_name: Extended_Data_Fig_7.zip
  file_size: 70694476
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 81e79a6d4e6745dce63cdad94bfcdca4
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:46:36Z
  date_updated: 2023-05-18T16:46:36Z
  file_id: '13026'
  file_name: Extended_Data_Fig_8b_T1.tif
  file_size: 57634426
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 53da2b10969a185239b317be0ffa61ef
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:48:26Z
  date_updated: 2023-05-18T16:48:26Z
  file_id: '13027'
  file_name: Extended_Data_Fig_8b_T2.tif
  file_size: 57634426
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9a97ccd3eb0c75a5c4f142e5dadc0fb3
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:02:09Z
  date_updated: 2023-05-18T15:02:09Z
  file_id: '12999'
  file_name: Extended_Data_Fig_8c_png.zip
  file_size: 2942961
  relation: main_file
  success: 1
- access_level: open_access
  checksum: baaee60e695160118ea2167c6cb91775
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:17:38Z
  date_updated: 2023-05-18T15:17:38Z
  file_id: '13008'
  file_name: Extended_Data_Fig9c_LIONESS.tif
  file_size: 11949362
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 095a980d0d746bc2277b0586dbb9d652
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:02:00Z
  date_updated: 2023-05-18T15:02:00Z
  file_id: '12998'
  file_name: Extended_Data_Fig_10_LIONESS_tif_xy_view.zip
  file_size: 72553526
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 343b87c4842eab9e5086f248668dec84
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:22:43Z
  date_updated: 2023-05-18T14:22:43Z
  file_id: '12992'
  file_name: Extended_Data_Fig_10_LIONESS_tif_xz_view.zip
  file_size: 72906090
  relation: main_file
  success: 1
- access_level: open_access
  checksum: c3d4970e5185f72cb89f36005e83a556
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:14:01Z
  date_updated: 2023-05-18T15:14:01Z
  file_id: '13004'
  file_name: Supplementary_Fig_4.zip
  file_size: 428208
  relation: main_file
  success: 1
- access_level: open_access
  checksum: f451852622f8ba8992582ab9b57c49e5
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:32:29Z
  date_updated: 2023-05-18T14:32:29Z
  file_id: '12991'
  file_name: Supplementary_Fig_8.zip
  file_size: 230506869
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 874b524f38fad6b86be14326bb5aa706
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T16:00:15Z
  date_updated: 2023-05-18T16:00:15Z
  file_id: '13019'
  file_name: Suppl_Fig_11_LIONESS.tif
  file_size: 40406386
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 7ab5cc6c581c463d1d7e430399b8b384
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:57:18Z
  date_updated: 2023-05-18T14:57:18Z
  file_id: '12996'
  file_name: Supplementary_Fig_12.zip
  file_size: 357705621
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 9763330288c2d544a3e1d7bc12657ee8
  content_type: image/tiff
  creator: jdanzl
  date_created: 2023-05-18T15:39:45Z
  date_updated: 2023-05-18T15:39:45Z
  file_id: '13009'
  file_name: Supplementary_Fig_13.tif
  file_size: 617709326
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1e83b64e220694942ccf0ca70f17e33b
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T14:19:48Z
  date_updated: 2023-05-18T14:19:48Z
  file_id: '12990'
  file_name: GCaMP_recording_overview_time_series_Suppl_Video_5.zip
  file_size: 9387873
  relation: main_file
  success: 1
- access_level: open_access
  checksum: fc7208299e6393e69b31a0051fa5ac2e
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:13:55Z
  date_updated: 2023-05-18T15:13:55Z
  file_id: '12993'
  file_name: CARE model.zip
  file_size: 1218458059
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 47db2185ff2c6ba9b059c9b1a8882832
  content_type: application/zip
  creator: jdanzl
  date_created: 2023-05-18T15:03:10Z
  date_updated: 2023-05-18T15:03:10Z
  file_id: '13000'
  file_name: Segmentation model.zip
  file_size: 19052980
  relation: main_file
  success: 1
file_date_updated: 2023-05-18T19:51:52Z
fulldoi: https://doi.org/10.15479/AT:ISTA:12817
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '13267'
    relation: used_in_publication
    status: public
status: public
title: Research data for the publication "Dense 4D nanoscale reconstruction of living
  brain tissue"
tmp:
  image: /images/cc_by_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
  name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
    BY-SA 4.0)
  short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14770'
abstract:
- lang: eng
  text: We developed LIONESS, a technology that leverages improvements to optical
    super-resolution microscopy and prior information on sample structure via machine
    learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio
    and light exposure) of optical microscopy of living biological specimens. LIONESS
    enables dense reconstruction of living brain tissue and morphodynamics visualization
    at the nanoscale.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Philipp
  full_name: Velicky, Philipp
  id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
  last_name: Velicky
  orcid: 0000-0002-2340-7431
citation:
  ama: Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living
    brain tissue. <i>Nature Methods</i>. 2023;20(8):1141-1142. doi:<a href="https://doi.org/10.1038/s41592-023-01937-5">10.1038/s41592-023-01937-5</a>
  apa: Danzl, J. G., &#38; Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction
    of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href="https://doi.org/10.1038/s41592-023-01937-5">https://doi.org/10.1038/s41592-023-01937-5</a>
  chicago: Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction
    of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href="https://doi.org/10.1038/s41592-023-01937-5">https://doi.org/10.1038/s41592-023-01937-5</a>.
  ieee: J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of
    living brain tissue,” <i>Nature Methods</i>, vol. 20, no. 8. Springer Nature,
    pp. 1141–1142, 2023.
  ista: Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of
    living brain tissue. Nature Methods. 20(8), 1141–1142.
  mla: Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction
    of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature,
    2023, pp. 1141–42, doi:<a href="https://doi.org/10.1038/s41592-023-01937-5">10.1038/s41592-023-01937-5</a>.
  short: J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.
corr_author: '1'
date_created: 2024-01-10T08:07:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-04-14T08:34:34Z
day: '01'
department:
- _id: JoDa
doi: 10.1038/s41592-023-01937-5
external_id:
  isi:
  - '001025621500002'
fulldoi: https://doi.org/10.1038/s41592-023-01937-5
intvolume: '        20'
isi: 1
issue: '8'
keyword:
- Cell Biology
- Molecular Biology
- Biochemistry
- Biotechnology
language:
- iso: eng
month: '08'
oa_version: None
page: 1141-1142
publication: Nature Methods
publication_identifier:
  eissn:
  - 1548-7105
  issn:
  - 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '13267'
    relation: extended_version
    status: public
scopus_import: '1'
status: public
title: LIONESS enables 4D nanoscale reconstruction of living brain tissue
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
OA_place: publisher
OA_type: hybrid
_id: '13267'
abstract:
- lang: eng
  text: Three-dimensional (3D) reconstruction of living brain tissue down to an individual
    synapse level would create opportunities for decoding the dynamics and structure–function
    relationships of the brain’s complex and dense information processing network;
    however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise
    ratio and prohibitive light burden in optical imaging, whereas electron microscopy
    is inherently static. Here we solved these challenges by developing an integrated
    optical/machine-learning technology, LIONESS (live information-optimized nanoscopy
    enabling saturated segmentation). This leverages optical modifications to stimulated
    emission depletion microscopy in comprehensively, extracellularly labeled tissue
    and previous information on sample structure via machine learning to simultaneously
    achieve isotropic super-resolution, high signal-to-noise ratio and compatibility
    with living tissue. This allows dense deep-learning-based instance segmentation
    and 3D reconstruction at a synapse level, incorporating molecular, activity and
    morphodynamic information. LIONESS opens up avenues for studying the dynamic functional
    (nano-)architecture of living brain tissue.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: E-Lib
- _id: LifeSc
- _id: M-Shop
acknowledgement: "We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance
  and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata
  for hardware control support and M. Cunha dos Santos for initial exploration of
  software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt,
  S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L.
  Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We
  acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and
  optics, preclinical, library and laboratory support facilities and by the Miba machine
  shop. We gratefully acknowledge funding by the following sources: Austrian Science
  Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.)
  and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung
  NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D.
  and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska
  Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research
  and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE
  (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.);
  and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research
  Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development
  grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship
  no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier
  Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science
  Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Philipp
  full_name: Velicky, Philipp
  id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
  last_name: Velicky
  orcid: 0000-0002-2340-7431
- first_name: Eder
  full_name: Miguel Villalba, Eder
  id: 3FB91342-F248-11E8-B48F-1D18A9856A87
  last_name: Miguel Villalba
  orcid: 0000-0001-5665-0430
- first_name: Julia M
  full_name: Michalska, Julia M
  id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
  last_name: Michalska
  orcid: 0000-0003-3862-1235
- first_name: Julia
  full_name: Lyudchik, Julia
  id: 46E28B80-F248-11E8-B48F-1D18A9856A87
  last_name: Lyudchik
- first_name: Donglai
  full_name: Wei, Donglai
  last_name: Wei
- first_name: Zudi
  full_name: Lin, Zudi
  last_name: Lin
- first_name: Jake
  full_name: Watson, Jake
  id: 63836096-4690-11EA-BD4E-32803DDC885E
  last_name: Watson
  orcid: 0000-0002-8698-3823
- first_name: Jakob
  full_name: Troidl, Jakob
  last_name: Troidl
- first_name: Johanna
  full_name: Beyer, Johanna
  last_name: Beyer
- first_name: Yoav
  full_name: Ben Simon, Yoav
  id: 43DF3136-F248-11E8-B48F-1D18A9856A87
  last_name: Ben Simon
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Wiebke
  full_name: Jahr, Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
  orcid: 0000-0003-0201-2315
- first_name: Alban
  full_name: Cenameri, Alban
  id: 9ac8f577-2357-11eb-997a-e566c5550886
  last_name: Cenameri
- first_name: Johannes
  full_name: Broichhagen, Johannes
  last_name: Broichhagen
- first_name: Seth G.N.
  full_name: Grant, Seth G.N.
  last_name: Grant
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Hanspeter
  full_name: Pfister, Hanspeter
  last_name: Pfister
- first_name: Bernd
  full_name: Bickel, Bernd
  id: 49876194-F248-11E8-B48F-1D18A9856A87
  last_name: Bickel
  orcid: 0000-0001-6511-9385
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction
    of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href="https://doi.org/10.1038/s41592-023-01936-6">10.1038/s41592-023-01936-6</a>
  apa: Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D.,
    Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain
    tissue. <i>Nature Methods</i>. Springer Nature. <a href="https://doi.org/10.1038/s41592-023-01936-6">https://doi.org/10.1038/s41592-023-01936-6</a>
  chicago: Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik,
    Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction
    of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href="https://doi.org/10.1038/s41592-023-01936-6">https://doi.org/10.1038/s41592-023-01936-6</a>.
  ieee: P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain
    tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.
  ista: Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson
    J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen
    J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense
    4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.
  mla: Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain
    Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a
    href="https://doi.org/10.1038/s41592-023-01936-6">10.1038/s41592-023-01936-6</a>.
  short: P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin,
    J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri,
    J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel,
    J.G. Danzl, Nature Methods 20 (2023) 1256–1265.
corr_author: '1'
date_created: 2023-07-23T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-10-02T11:27:12Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
- _id: GaNo
- _id: BeBi
- _id: JoDa
- _id: Bio
doi: 10.1038/s41592-023-01936-6
ec_funded: 1
external_id:
  isi:
  - '001025621500001'
  pmid:
  - '37429995'
file:
- access_level: open_access
  checksum: a68e845780a82ea36d0d4d3212a87c10
  content_type: application/pdf
  creator: dernst
  date_created: 2025-02-26T08:01:57Z
  date_updated: 2025-02-26T08:01:57Z
  file_id: '19088'
  file_name: 2023_NatureMethods_Velicky.pdf
  file_size: 14103039
  relation: main_file
  success: 1
file_date_updated: 2025-02-26T08:01:57Z
fulldoi: https://doi.org/10.1038/s41592-023-01936-6
has_accepted_license: '1'
intvolume: '        20'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1256-1265
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I03600
  name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00312
  name: Synaptic communication in neuronal microcircuits
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
  grant_number: LS18-022
  name: High content imaging to decode human immune cell interactions in health and
    allergic disease
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715767'
  name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
    Modeling'
- _id: 25444568-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715508'
  name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
    and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '692692'
  name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
  call_identifier: H2020
  grant_number: '101026635'
  name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
  grant_number: LT00057
  name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Nature Methods
publication_identifier:
  eissn:
  - 1548-7105
  issn:
  - 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/danzllab/LIONESS
  record:
  - id: '12817'
    relation: research_data
    status: public
  - id: '14770'
    relation: shorter_version
    status: public
  - id: '11943'
    relation: earlier_version
    status: public
  - id: '18674'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Dense 4D nanoscale reconstruction of living brain tissue
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...