---
_id: '10290'
abstract:
- lang: eng
  text: A precise quantitative description of the ultrastructural characteristics
    underlying biological mechanisms is often key to their understanding. This is
    particularly true for dynamic extra- and intracellular filamentous assemblies,
    playing a role in cell motility, cell integrity, cytokinesis, tissue formation
    and maintenance. For example, genetic manipulation or modulation of actin regulatory
    proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
    architecture of actin filament-rich cell peripheral structures, such as lamellipodia
    or filopodia. However, the observed ultrastructural effects often remain subtle
    and require sufficiently large datasets for appropriate quantitative analysis.
    The acquisition of such large datasets has been enabled by recent advances in
    high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
    the development of complementary approaches to maximize the extraction of relevant
    biological information. We have developed a computational toolbox for the semi-automatic
    quantification of segmented and vectorized filamentous networks from pre-processed
    cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
    experimental conditions. GUI-based components simplify the processing of data
    and allow users to obtain a large number of ultrastructural parameters describing
    filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
    cryo-ET data of untreated and chemically perturbed branched actin filament networks
    and that of parallel actin filament arrays. In principle, the computational toolbox
    presented here is applicable for data analysis comprising any type of filaments
    in regular (i.e. parallel) or random arrangement. We show that it can ease the
    identification of key differences between experimental groups and facilitate the
    in-depth analysis of ultrastructural data in a time-efficient manner.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: 'This research was supported by the Scientific Service Units (SSUs)
  of IST Austria through resources provided by Scientific Computing (SciComp), the
  Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
  Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data
  acquisition. The authors acknowledge support from IST Austria and from the Austrian
  Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.'
article_number: '107808'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Georgi A
  full_name: Dimchev, Georgi A
  id: 38C393BE-F248-11E8-B48F-1D18A9856A87
  last_name: Dimchev
  orcid: 0000-0001-8370-6161
- first_name: Behnam
  full_name: Amiri, Behnam
  last_name: Amiri
- first_name: Florian
  full_name: Fäßler, Florian
  id: 404F5528-F248-11E8-B48F-1D18A9856A87
  last_name: Fäßler
  orcid: 0000-0001-7149-769X
- first_name: Martin
  full_name: Falcke, Martin
  last_name: Falcke
- first_name: Florian KM
  full_name: Schur, Florian KM
  id: 48AD8942-F248-11E8-B48F-1D18A9856A87
  last_name: Schur
  orcid: 0000-0003-4790-8078
citation:
  ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
    ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal
    of Structural Biology</i>. 2021;213(4). doi:<a href="https://doi.org/10.1016/j.jsb.2021.107808">10.1016/j.jsb.2021.107808</a>
  apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021).
    Computational toolbox for ultrastructural quantitative analysis of filament networks
    in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier . <a href="https://doi.org/10.1016/j.jsb.2021.107808">https://doi.org/10.1016/j.jsb.2021.107808</a>
  chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
    KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
    Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier
    , 2021. <a href="https://doi.org/10.1016/j.jsb.2021.107808">https://doi.org/10.1016/j.jsb.2021.107808</a>.
  ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
    toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
    data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier , 2021.
  ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox
    for ultrastructural quantitative analysis of filament networks in cryo-ET data.
    Journal of Structural Biology. 213(4), 107808.
  mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative
    Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>,
    vol. 213, no. 4, 107808, Elsevier , 2021, doi:<a href="https://doi.org/10.1016/j.jsb.2021.107808">10.1016/j.jsb.2021.107808</a>.
  short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural
    Biology 213 (2021).
corr_author: '1'
date_created: 2021-11-15T12:21:42Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2025-04-15T08:25:41Z
day: '03'
ddc:
- '572'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2021.107808
external_id:
  isi:
  - '000720259500002'
file:
- access_level: open_access
  checksum: 6b209e4d44775d4e02b50f78982c15fa
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-11-15T13:11:27Z
  date_updated: 2021-11-15T13:11:27Z
  file_id: '10291'
  file_name: 2021_JournalStructBiol_Dimchev.pdf
  file_size: 16818304
  relation: main_file
  success: 1
file_date_updated: 2021-11-15T13:11:27Z
has_accepted_license: '1'
intvolume: '       213'
isi: 1
issue: '4'
keyword:
- Structural Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
  grant_number: P33367
  name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02495
  name: Protein structure and function in filopodia across scales
publication: Journal of Structural Biology
publication_identifier:
  issn:
  - 1047-8477
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
related_material:
  record:
  - id: '14502'
    relation: software
    status: public
scopus_import: '1'
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
  networks in cryo-ET data
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: 213
year: '2021'
...