---
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:<a href="https://doi.org/10.15479/at:ista:12470">10.15479/at:ista:12470</a>
  apa: Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis
    of nervous tissue organization with light microscopy</i>. Institute of Science
    and Technology Austria. <a href="https://doi.org/10.15479/at:ista:12470">https://doi.org/10.15479/at:ista:12470</a>
  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. <a href="https://doi.org/10.15479/at:ista:12470">https://doi.org/10.15479/at:ista:12470</a>.
  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. <i>A Versatile Toolbox for the Comprehensive Analysis of
    Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and
    Technology Austria, 2023, doi:<a href="https://doi.org/10.15479/at:ista:12470">10.15479/at:ista:12470</a>.
  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'
date_created: 2023-01-31T15:10:53Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2026-04-07T14:11:10Z
day: '09'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:12470
ec_funded: 1
file:
- access_level: open_access
  checksum: 1a2306e5f59f52df598e7ecfadf921ac
  content_type: application/pdf
  creator: cchlebak
  date_created: 2023-01-31T15:11:42Z
  date_updated: 2023-07-27T22:30:54Z
  embargo: 2023-07-09
  file_id: '12471'
  file_name: 20230109_PhD_thesis_JM_final.pdf
  file_size: 41771714
  relation: main_file
- access_level: closed
  checksum: 0bebbdee0773443959e1f6ab8caf281f
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: cchlebak
  date_created: 2023-01-31T15:11:51Z
  date_updated: 2023-07-10T22:30:04Z
  embargo_to: open_access
  file_id: '12472'
  file_name: 20230109_PhD_thesis_JM_final.docx
  file_size: 66983464
  relation: source_file
file_date_updated: 2023-07-27T22:30:54Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '201'
project:
- _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
publication_identifier:
  isbn:
  - 978-3-99078-026-8
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '11943'
    relation: part_of_dissertation
    status: public
  - id: '11950'
    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: A versatile toolbox for the comprehensive analysis of nervous tissue organization
  with light 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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...