epitools
Quantifying 2D cell shape and epithelial tissue dynamics
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 5 committers (60.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Quantifying 2D cell shape and epithelial tissue dynamics
Basic Info
- Host: GitHub
- Owner: epitools
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://pypi.org/project/epitools
- Size: 115 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 1
- Open Issues: 26
- Releases: 13
Topics
Metadata Files
README.md
Welcome to EpiTools!
EpiTools is a Python package and associated napari plugin to extract the membrane signal from epithelial tissues and analyze it with the aid of computer vision.
The development of EpiTools was inspired by the challenges in analyzing time-lapses of growing Drosophila imaginal discs.
The folded morphology, the very small apical cell surfaces and the long time series required a new automated cell recognition to accurately study growth dynamics.
Installation
First, install napari.
The recommended way to install EpiTools is via
pip
sh
python -m pip install epitools
To install the latest development version of EpiTools clone this repository
and run
sh
python -m pip install -e .
If working on Apple Silicon make sure to also install the following package from conda-forge.
sh
conda install -c conda-forge pyqt
Recommended Companion Napari Plugins
To also install the recommended plugins for the EpiTools workflow run
sh
python -m pip install epitools[wf]
and
sh
python -m pip install -e .[wf]
When installing with Apple Mac OS X terminal, you might need to add '"' to [wf] as in:
sh
python -m pip install -e ."[wf]"
If working on Apple Silicon make sure to also install the following package from conda-forge
sh
conda install -c conda-forge cvxopt
which is required for btrack.
Issues
If you encounter any problems, please file an issue along with a detailed description.
Contributing
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Owner
- Name: EpiTools
- Login: epitools
- Kind: organization
- Website: epitools.github.io
- Repositories: 10
- Profile: https://github.com/epitools
An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 'EpiTools: image toolkit for epithelia'
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Paddy
family-names: Roddy
affiliation: >-
Advanced Research Computing, University College
London, London
- given-names: Daniel
family-names: Matthews
affiliation: >-
Advanced Research Computing, University College
London, London
- given-names: Paul
name-particle: J
family-names: Smith
affiliation: >-
Advanced Research Computing, University College
London, London
- given-names: Alessandro
family-names: Felder
affiliation: >-
Advanced Research Computing, University College
London, London
- given-names: Pablo
family-names: Vicente Munuera
email: p.munuera@ucl.ac.uk
affiliation: >-
Laboratory for Molecular Cell Biology, University
College London, London
orcid: 'https://orcid.org/0000-0001-5402-7637'
- given-names: Giulia
family-names: Paci
email: g.paci@ucl.ac.uk
affiliation: >-
Laboratory for Molecular Cell Biology, University
College London, London
orcid: 'https://orcid.org/0000-0003-0565-4356'
- given-names: Yanlan
family-names: Mao
email: y.mao@ucl.ac.uk
affiliation: >-
Laboratory for Molecular Cell Biology, University
College London, London
orcid: 'https://orcid.org/0000-0002-8722-4992'
repository-code: 'https://github.com/epitools/epitools'
url: 'https://www.napari-hub.org/plugins/epitools'
repository: 'https://pypi.org/project/epitools/'
abstract: Quantifying 2D cell shape and epithelial tissue dynamics.
keywords:
- Image analysis
- Cell
- Epithelial tissue
- Segmentation
- Dynamics
license: BSD-3-Clause
commit: 0db3256fa368aad8fb00a0d9cf3dbfedb88817c8
version: 0.0.13
date-released: '2025-01-27'
GitHub Events
Total
- Create event: 3
- Release event: 1
- Issues event: 6
- Watch event: 1
- Delete event: 1
- Issue comment event: 3
- Push event: 16
- Pull request event: 4
Last Year
- Create event: 3
- Release event: 1
- Issues event: 6
- Watch event: 1
- Delete event: 1
- Issue comment event: 3
- Push event: 16
- Pull request event: 4
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel Matthews | d****s@u****k | 88 |
| Patrick Roddy | p****y@g****m | 21 |
| Paul Smith | p****h@u****k | 19 |
| Pablo Vicente Munuera | p****a@u****k | 9 |
| Giulia Paci | 3****i | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 85
- Total pull requests: 63
- Average time to close issues: about 1 month
- Average time to close pull requests: 21 days
- Total issue authors: 8
- Total pull request authors: 5
- Average comments per issue: 0.45
- Average comments per pull request: 1.02
- Merged pull requests: 59
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 3
- Average time to close issues: 12 days
- Average time to close pull requests: 5 days
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.67
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- paddyroddy (30)
- Pablo1990 (19)
- drmatthews (11)
- p-j-smith (10)
- giuliapaci (4)
- alessandrofelder (1)
- kephale (1)
- goanpeca (1)
Pull Request Authors
- paddyroddy (19)
- p-j-smith (17)
- Pablo1990 (16)
- drmatthews (4)
- giuliapaci (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 45 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 13
- Total maintainers: 1
pypi.org: epitools
Quantifying 2D cell shape and epithelial tissue dynamics
- Homepage: https://www.ucl.ac.uk/lmcb/users/yanlan-mao
- Documentation: https://epitools.readthedocs.io/
- License: BSD 3-Clause Licence Copyright (c) 2022-2023, EpiTools Developers All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
Latest release: 0.0.13
published about 1 year ago