Published July 31, 2025
| Version v1
Software
Open
VesiclePy: A Comprehensive Vesicle Analysis Toolbox for Volume Electron Microscopy
Authors/Creators
-
Adhinarta, Jason
(Project member)1
-
Fan, Yutian
(Project member)1
-
Gohain, Adam
(Project member)1
-
Lin, Michael
(Project member)1
-
Nurkin, Paige
(Data curator)2
- Ren, Richard (Project member)2
-
Roth, Micaela
(Project member)1
- Zhang, Shulin (Project manager)2
- Yakobe, Ayal (Project member)2
- Yuste, Rafael (Project leader)2
-
Wei, Donglai
(Project leader)1
-
1.
Boston College
-
2.
Columbia University
Description
VesiclePy is a deep learning toolkit for vesicle analysis in serial electron microscopy data (with a special focus on large vesicles outside of synapse), providing tools for segmentation, classification, spatial and statistical analysis of vesicles, along with web-based proofreading tools and visualization capabilities, as well as neuron classification with vesicle and morphology information.
see README.md files, both the main one and those in subfolders, for usage instructions. documentation also available in code itself.
Files
VesiclePy.zip
Files
(791.0 MB)
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md5:d950864b012df8b1b971644bf230b4d0
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Additional details
Funding
- U.S. National Science Foundation
- CAREER: Scaling up Brain Circuit Reconstruction with Human-centric Machine Learning 2239688
- U.S. National Science Foundation
- CRCNS Research Project: Solving the neural code of Hydra 1822550
- U.S. National Science Foundation
- NSF-ANR: REBIRTH: Understanding The Self-Assembly Of The Nervous System of Hydra Vulgaris 2203119
- United States Department of Defense
- Vannevar Bush Faculty Award: Reprogramming the Nervous System of a Cnidarian ONR N000142012828
Software
- Repository URL
- https://github.com/PytorchConnectomics/VesiclePy
- Programming language
- Python
- Development Status
- Active