Cryo-electron tomography (cryo-ET) has the potential to reveal cell structure down to atomic resolution. Nevertheless, cellular cryo-ET data is highly complex, requiring image segmentation for visualization and quantification of subcellular structures. Due to noise and anisotropic resolution in cryo-ET data, automatic segmentation based on classical computer vision approaches usually does not perform satisfactorily. Communication between neurons relies on neurotransmitter-filled synaptic vesicle (SV) exocytosis. Cryo-ET study of the spatial organization of SVs and their interconnections allows a better understanding of the mechanisms of exocytosis regulation. Accurate SV segmentation is a prerequisite to obtaining a faithful connectivity representation. Hundreds of SVs are present in a synapse, and their manual segmentation is a bottleneck. We addressed this by designing a workflow consisting of a convolutional network followed by post-processing steps. Alongside, we provide an interactive tool for accurately segmenting spherical vesicles. Our pipeline can in principle segment spherical vesicles in any cell type as well as extracellular and in vitro spherical vesicles.
Skip Nav Destination
Article navigation
Tools|
October 24 2024
CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms
Amin Khosrozadeh
,
Amin Khosrozadeh
(Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing - original draft, Writing - review & editing)
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
2
Graduate School for Cellular and Biomedical Sciences, University of Bern
, Bern, Switzerland
Search for other works by this author on:
Raphaela Seeger
,
Raphaela Seeger
(Data curation, Formal analysis, Investigation, Validation, Visualization, Writing - original draft)
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
2
Graduate School for Cellular and Biomedical Sciences, University of Bern
, Bern, Switzerland
Search for other works by this author on:
Guillaume Witz
,
Guillaume Witz
(Methodology, Software)
3
Data Science Lab, University of Bern
, Bern, Switzerland
Search for other works by this author on:
Julika Radecke
,
Julika Radecke
(Investigation, Resources, Writing - review & editing)
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
4Department of Neuroscience,
Faculty of Health and Medical Science, University of Copenhagen
, Copenhagen, Denmark
5
Diamond Light Source Ltd.
, Didcot, UK
Search for other works by this author on:
Jakob B. Sørensen
,
Jakob B. Sørensen
(Resources, Writing - review & editing)
6Department of Neuroscience,
University of Copenhagen
, Copenhagen, Denmark
Search for other works by this author on:
Benoît Zuber
(Conceptualization, Data curation, Formal analysis, Funding acquisition, Methodology, Project administration, Software, Supervision, Writing - review & editing)
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
Correspondence to Benoît Zuber: [email protected]
Search for other works by this author on:
Amin Khosrozadeh
Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing - original draft, Writing - review & editing
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
2
Graduate School for Cellular and Biomedical Sciences, University of Bern
, Bern, Switzerland
Raphaela Seeger
Data curation, Formal analysis, Investigation, Validation, Visualization, Writing - original draft
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
2
Graduate School for Cellular and Biomedical Sciences, University of Bern
, Bern, Switzerland
Guillaume Witz
Methodology, Software
3
Data Science Lab, University of Bern
, Bern, Switzerland
Julika Radecke
Investigation, Resources, Writing - review & editing
1
Institute of Anatomy, University of Bern
, Bern, Switzerland
4Department of Neuroscience,
Faculty of Health and Medical Science, University of Copenhagen
, Copenhagen, Denmark
5
Diamond Light Source Ltd.
, Didcot, UK
Jakob B. Sørensen
Resources, Writing - review & editing
6Department of Neuroscience,
University of Copenhagen
, Copenhagen, Denmark
Correspondence to Benoît Zuber: [email protected]
Disclosures: The authors declare no competing interests exist.
Received:
March 04 2024
Revision Received:
July 26 2024
Accepted:
September 20 2024
Online ISSN: 1540-8140
Print ISSN: 0021-9525
Funder(s):
Swiss National Science Foundation
- Award Id(s): 179520
Funder(s):
ERA-NET NEURON
- Award Id(s): NEURON-119
Funder(s):
University of Bern Research Foundation
© 2024 Khosrozadeh et al.
2024
Khosrozadeh et al.
This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).
J Cell Biol (2025) 224 (1): e202402169.
Article history
Received:
March 04 2024
Revision Received:
July 26 2024
Accepted:
September 20 2024
Citation
Amin Khosrozadeh, Raphaela Seeger, Guillaume Witz, Julika Radecke, Jakob B. Sørensen, Benoît Zuber; CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms. J Cell Biol 6 January 2025; 224 (1): e202402169. doi: https://doi.org/10.1083/jcb.202402169
Download citation file:
Sign in
Don't already have an account? Register
Client Account
You could not be signed in. Please check your email address / username and password and try again.
Could not validate captcha. Please try again.
Sign in via your Institution
Sign in via your Institution
408
Views
Suggested Content
Email alerts
Advertisement
Advertisement