---
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
- 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: 2025-10-08T08:43:56Z
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
has_accepted_license: '1'
intvolume: '        37'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
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: '18689'
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    status: public
  - id: '18837'
    relation: research_data
    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'
...
---
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>. Elsevier. <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>. Elsevier, 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. Elsevier, 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, Elsevier, 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: 2026-04-07T11:48:07Z
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:
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  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'
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  file_size: 7238179
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file_date_updated: 2025-06-10T07:24:46Z
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: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '20206'
    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
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: 2026-04-28T13:33:34Z
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
has_accepted_license: '1'
intvolume: '       642'
isi: 1
language:
- iso: eng
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: '18677'
    relation: earlier_version
    status: public
  - id: '18697'
    relation: research_data
    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: 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'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-04-07T12:56:36Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
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
status: public
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
date_created: 2024-12-18T14:48:24Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '08'
department:
- _id: GaNo
- _id: JoDa
doi: 10.1101/2024.03.01.582884
ec_funded: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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
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  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
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  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
related_material:
  record:
  - id: '18681'
    relation: dissertation_contains
    status: public
  - id: '18674'
    relation: dissertation_contains
    status: public
  - id: '19704'
    relation: later_version
    status: public
status: public
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: 2026-04-14T08:34:37Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18471
ec_funded: 1
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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
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: 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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...