---
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: 1st International Workshop on
Efficient Medical Artificial Intelligence. Vol 16318. Springer Nature; 2026:257-267.
doi:10.1007/978-3-032-13961-0_26'
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 1st International Workshop on Efficient Medical Artificial
Intelligence (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature.
https://doi.org/10.1007/978-3-032-13961-0_26'
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 1st International
Workshop on Efficient Medical Artificial Intelligence, 16318:257–67. Springer
Nature, 2026. https://doi.org/10.1007/978-3-032-13961-0_26.'
ieee: 'J. Troidl et al., “niiv: Interactive Self-supervised Neural Implicit
Isotropic Volume Reconstruction,” in 1st International Workshop on Efficient
Medical Artificial Intelligence, 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.” 1st International Workshop on Efficient Medical Artificial
Intelligence, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:10.1007/978-3-032-13961-0_26.'
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
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: 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. The Plant Cell. 2025;37(4). doi:10.1093/plcell/koaf006
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. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koaf006
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.” The Plant Cell. Oxford University
Press, 2025. https://doi.org/10.1093/plcell/koaf006.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” The Plant Cell, 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.” The Plant Cell, vol. 37, no. 4, koaf006, Oxford University Press,
2025, doi:10.1093/plcell/koaf006.
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
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'
relation: earlier_version
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. Biophysical Reports. 2025;5(2).
doi:10.1016/j.bpr.2025.100211
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. Biophysical Reports. Elsevier. https://doi.org/10.1016/j.bpr.2025.100211
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.” Biophysical
Reports. Elsevier, 2025. https://doi.org/10.1016/j.bpr.2025.100211.
ieee: J. Vorlaufer et al., “Image-based 3D active sample stabilization on
the nanometer scale for optical microscopy,” Biophysical Reports, 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.” Biophysical Reports, vol. 5, no.
2, 100211, Elsevier, 2025, doi:10.1016/j.bpr.2025.100211.
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:
- 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
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
_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. Cell. 2025;188(2):501-514.e18.
doi:10.1016/j.cell.2024.11.022
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. Cell. Elsevier. https://doi.org/10.1016/j.cell.2024.11.022
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.” Cell. Elsevier, 2025. https://doi.org/10.1016/j.cell.2024.11.022.
ieee: J. Watson et al., “Human hippocampal CA3 uses specific functional connectivity
rules for efficient associative memory,” Cell, vol. 188, no. 2. Elsevier,
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.” Cell, vol. 188, no. 2, Elsevier,
2025, p. 501–514.e18, doi:10.1016/j.cell.2024.11.022.
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: 2026-04-14T08:34:32Z
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
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: Elsevier
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'
...
---
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. Nature. 2025;642:398-410. doi:10.1038/s41586-025-08985-1
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. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08985-1
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.” Nature. Springer
Nature, 2025. https://doi.org/10.1038/s41586-025-08985-1.
ieee: M. Tavakoli et al., “Light-microscopy-based connectomic reconstruction
of mammalian brain tissue,” Nature, 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.” Nature, vol. 642, Springer Nature, 2025, pp.
398–410, doi:10.1038/s41586-025-08985-1.
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. bioRxiv. doi:10.1101/2024.02.21.581330
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. bioRxiv. https://doi.org/10.1101/2024.02.21.581330
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.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.21.581330.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” bioRxiv. .
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,
10.1101/2024.02.21.581330.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” BioRxiv, doi:10.1101/2024.02.21.581330.
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
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_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:10.15479/at:ista:18681'
apa: '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. https://doi.org/10.15479/at:ista:18681'
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. https://doi.org/10.15479/at:ista:18681.'
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. 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, doi:10.15479/at:ista:18681.'
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'
date_created: 2024-12-19T02:30:39Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-04-07T12:56:37Z
day: '20'
ddc:
- '600'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18681
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creator: mtavakol
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date_updated: 2024-12-20T10:25:12Z
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embargo_to: open_access
file_id: '18700'
file_name: Thesis_Mojtaba Tavakoli_.pdf
file_size: 63885521
relation: main_file
file_date_updated: 2024-12-20T10:31:37Z
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: '18677'
relation: part_of_dissertation
status: public
- id: '18689'
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: '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: ba8df636-2132-11f1-aed0-ed93e2281fdd
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. bioRxiv.
doi:10.1101/2024.05.02.592169
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. bioRxiv. https://doi.org/10.1101/2024.05.02.592169
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.” BioRxiv, n.d. https://doi.org/10.1101/2024.05.02.592169.
ieee: J. F. Watson et al., “Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory,” bioRxiv. .
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, 10.1101/2024.05.02.592169.
mla: Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity
Rules for Efficient Associative Memory.” BioRxiv, doi:10.1101/2024.05.02.592169.
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: 2026-04-14T08:34:32Z
day: '02'
department:
- _id: JoDa
- _id: PeJo
doi: 10.1101/2024.05.02.592169
ec_funded: 1
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: 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. bioRxiv. doi:10.1101/2024.03.01.582884
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. bioRxiv. https://doi.org/10.1101/2024.03.01.582884
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.” BioRxiv,
n.d. https://doi.org/10.1101/2024.03.01.582884.
ieee: M. Tavakoli et al., “Light-microscopy based dense connectomic reconstruction
of mammalian brain tissue,” bioRxiv. .
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, 10.1101/2024.03.01.582884.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction
of Mammalian Brain Tissue.” BioRxiv, doi:10.1101/2024.03.01.582884.
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
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: '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'
...
---
_id: '11160'
abstract:
- lang: eng
text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent
cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses
macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency
affects neurodevelopmental is unclear. Here, employing human cerebral organoids,
we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories
with an accelerated and delayed generation of, respectively, inhibitory and excitatory
neurons that yields, at days 60 and 120, symmetrically opposite expansions in
their proportions. This imbalance is consistent with an enlargement of cerebral
organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic
design of patient-specific mutations and mosaic organoids, we define genotype-phenotype
relationships and uncover their cell-autonomous nature. Our results define cell-type-specific
CHD8-dependent molecular defects related to an abnormal program of proliferation
and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations,
our study uncovers reproducible developmental alterations that may be employed
for neurodevelopmental disease modeling.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Farnaz Freeman for technical assistance. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This
work supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs);
the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele;
and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures
were created using BioRender.com.
article_number: '110615'
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlo Emanuele
full_name: Villa, Carlo Emanuele
last_name: Villa
- first_name: Cristina
full_name: Cheroni, Cristina
last_name: Cheroni
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Alejandro
full_name: López-Tóbon, Alejandro
last_name: López-Tóbon
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Michele
full_name: Gabriele, Michele
last_name: Gabriele
- 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: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mariano
full_name: Gabitto, Mariano
last_name: Gabitto
- 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: Giuseppe
full_name: Testa, Giuseppe
last_name: Testa
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism
to transient alterations in excitatory and inhibitory trajectories. Cell Reports.
2022;39(1). doi:10.1016/j.celrep.2022.110615
apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco,
R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615
chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon,
Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency
Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.”
Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615.
ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient
alterations in excitatory and inhibitory trajectories,” Cell Reports, vol.
39, no. 1. Elsevier, 2022.
ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ,
Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG,
Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.
mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient
Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol.
39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615.
short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco,
A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer,
M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).
corr_author: '1'
date_created: 2022-04-15T09:03:10Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2026-04-29T22:30:31Z
day: '05'
ddc:
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department:
- _id: JoDa
- _id: GaNo
doi: 10.1016/j.celrep.2022.110615
ec_funded: 1
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title: CHD8 haploinsufficiency links autism to transient alterations in excitatory
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