---
OA_place: publisher
_id: '20206'
abstract:
- lang: eng
text: "The internal structure of biomolecules and their organization in higher-order
arrangements are key factors governing the working principles of biological systems.
Bioimaging has successfully revealed arrangements across relevant spatial scales.
For example, cryo-electron tomography has become widely used for analyzing biomolecular
structures in situ due to its comprehensive structural visualization of near-natively
preserved samples, and its capability of sub-nm resolution via averaging. However,
the identification of molecules within crowded cellular environments is often
hindered by low contrast. Fluorescence microscopy, on the other hand, routinely
visualizes specifically labeled targets at single-molecule contrast against essentially
zero background. Moreover, it provides comparatively high throughput and is amenable
to multiplexing. Due to this complementarity, combining datasets from both modalities
acquired on the same region via correlative light and electron microscopy can
reveal novel types of information. \r\nThe spatial scale at which information
can be extracted depends on imaging resolution and correlation accuracy. Since
diffraction of light limits the resolution of conventional fluorescence microscopy
to few hundreds of nanometers, reaching the full potential of correlative imaging
requires super-resolution approaches. Performing imaging at cryogenic temperature
preserves structures in a near-native state and minimizes distortions between
the fluorescence and the electron microscopy datasets. Implementations of this
concept have achieved correlation on the scale of cellular organelles or bacterial
domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule
scale by improving cryo-super-resolution microscopy, and devising a refined image
correlation workflow. As part of this project, I constructed a microscopy setup
and adopted it for super-resolution fluorescence microscopy at room temperature
and cryogenic conditions. I explored different cryo-stages and acquisition strategies.
Specifically, I developed a new scheme for correcting sample drift, thus increasing
mechanical stability during microscopy acquisitions.\r\n"
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: Bio
acknowledgement: "The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI:
https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised
fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989),
as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary
Project Committee. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
citation:
ama: Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in
situ structure analysis. 2025. doi:10.15479/AT-ISTA-20206
apa: Vorlaufer, J. (2025). Construction of a cryo-super-resolution microscope
to guide in situ structure analysis. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20206
chicago: Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to
Guide in Situ Structure Analysis.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-20206.
ieee: J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide
in situ structure analysis,” Institute of Science and Technology Austria, 2025.
ista: Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide
in situ structure analysis. Institute of Science and Technology Austria.
mla: Vorlaufer, Jakob. Construction of a Cryo-Super-Resolution Microscope to
Guide in Situ Structure Analysis. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-20206.
short: J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide
in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-22T08:12:55Z
date_published: 2025-08-25T00:00:00Z
date_updated: 2026-04-07T11:48:07Z
day: '25'
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- _id: JoDa
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month: '08'
oa: 1
oa_version: Published Version
page: '107'
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- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
status: public
supervisor:
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full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: Construction of a cryo-super-resolution microscope to guide in situ structure
analysis
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...
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_id: '18681'
acknowledged_ssus:
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- _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'
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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:
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- id: '18688'
relation: part_of_dissertation
status: public
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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'
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user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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...
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OA_place: publisher
_id: '18674'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue requires volumetric imaging at nanoscale spatial resolution. While
light microscopy excels at visualizing specific molecules and individual cells,
achieving dense, synapse-level circuit reconstruction has not been possible with
any light microscopy technique. Thus, the goal of my work was to develop image
and data analysis pipelines for brain tissue visualization and reconstruction
with light microscopy. To achieve dense circuit reconstruction with single-synapse
resolution, I developed both conventional and deep-learning-based synapse detection
algorithms, as well as connectivity analysis pipelines that integrate synapse
detection with volumetric segmentation of brain tissue.
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
citation:
ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. 2024. doi:10.15479/at:ista:18674
apa: Lyudchik, J. (2024). Image analysis for brain tissue reconstruction with
super-resolution light microscopy. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18674
chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18674.
ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution
light microscopy,” Institute of Science and Technology Austria, 2024.
ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. Institute of Science and Technology Austria.
mla: Lyudchik, Julia. Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18674.
short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-12-18T14:24:43Z
date_published: 2024-12-18T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '18'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18674
ec_funded: 1
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date_created: 2024-12-18T14:21:06Z
date_updated: 2024-12-18T14:41:53Z
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file_name: 18122024_PhDthesis_corrected_final_JL_markup.docx
file_size: 99172203
relation: source_file
file_date_updated: 2024-12-18T14:41:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '217'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- ' 978-3-99078-051-0'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11160'
relation: part_of_dissertation
status: public
- id: '18677'
relation: part_of_dissertation
status: public
- id: '13267'
relation: part_of_dissertation
status: public
- id: '14257'
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: Image analysis for brain tissue reconstruction with super-resolution light
microscopy
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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...
---
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:10.15479/at:ista:18471
apa: Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape
with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471
chicago: Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape
with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471.
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. Visualizing the Neuronal Transcriptional Landscape
with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471.
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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file_date_updated: 2025-05-05T22:30:04Z
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
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...
---
OA_place: publisher
_id: '12470'
abstract:
- lang: eng
text: "The brain is an exceptionally sophisticated organ consisting of billions
of cells and trillions of \r\nconnections that orchestrate our cognition and behavior.
To decode its complex connectivity, it is \r\npivotal to disentangle its intricate
architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo
achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue
across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous
tissue context with (super\x02resolution) fluorescence microscopy. CATS combines
comprehensive labeling of the extracellular\r\nspace, that is compatible with
chemical fixation, with information on molecular markers, super\x02resolved data
acquisition and machine-learning based data analysis for segmentation and synapse
\r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity,
ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down
to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified
synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity
pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows
that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with
light microscopy."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: EM-Fac
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
citation:
ama: Michalska JM. A versatile toolbox for the comprehensive analysis of nervous
tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470
apa: Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis
of nervous tissue organization with light microscopy. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12470
chicago: Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis
of Nervous Tissue Organization with Light Microscopy.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.
ieee: J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous
tissue organization with light microscopy,” Institute of Science and Technology
Austria, 2023.
ista: Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of
nervous tissue organization with light microscopy. Institute of Science and Technology
Austria.
mla: Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of
Nervous Tissue Organization with Light Microscopy. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:12470.
short: J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous
Tissue Organization with Light Microscopy, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
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supervisor:
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id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: A versatile toolbox for the comprehensive analysis of nervous tissue organization
with light microscopy
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name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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...