tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
3 of 31 committers (9.7%) from academic institutions -
✓Institutional organization owner
Organization tissueimageanalytics has institutional domain (warwick.ac.uk) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Basic Info
- Host: GitHub
- Owner: TissueImageAnalytics
- License: other
- Language: Python
- Default Branch: develop
- Homepage: https://warwick.ac.uk/tia
- Size: 501 MB
Statistics
- Stars: 461
- Watchers: 8
- Forks: 95
- Open Issues: 20
- Releases: 26
Topics
Metadata Files
README.md
TIA Toolbox
Computational Pathology Toolbox developed at the TIA Centre
Getting Started
TIAToolbox is a computational pathology toolbox developed by the TIA Centre. It provides an end-to-end API for pathology image analysis using best practices. Based on PyTorch, a popular deep learning framework, TIAToolbox enables efficient and flexible implementation of state-of-the-art algorithms. It supports many features through a command-line interface and can integrate with standard PyTorch modules. The toolbox offers tools for data loading, pre-processing, model inference, post-processing, and visualization. Whether you are a computational, biomedical, or clinical researcher, TIAToolbox can help you get started in digital pathology with minimal effort.
All Users
This package is designed for those interested in digital pathology, including graduate students, medical staff, members of the TIA Centre and PathLAKE, and anyone who may find it useful. We will continue to improve this package, taking into account developments in pathology, microscopy, computing, and related disciplines. Please send comments and feedback to tia@dcs.warwick.ac.uk.
Developers
If you want to contribute to this repository, please first look at our Wiki and our contributor guidelines. Also, see the Prepare for development section of this document.
Useful Links
The bash shell is available on all commonly encountered platforms. Commands in this README are in bash. Windows users can use the command prompt to install conda and Python packages.
conda is a management system for software packages and virtual environments. To get conda, download Anaconda, which includes hundreds of the most useful Python packages, using 2GB of disk space. Alternatively, miniconda uses 400MB, and packages can be added as needed.
Examples Taster
- Click here for jupyter notebooks, hosted on the web, with demos of
tiatoolbox. All necessary resources to run the notebooks are remotely provided, so you don't need to have Python installed on your computer. - Click on a filename with suffix
.ipynband the notebook will open in your browser. - Click on one of the two blue checkboxes in your browser window labelled either Open in Colab or Open in Kaggle: colab and kaggle are websites providing free-of-charge platforms for running jupyter notebooks.
- Operate the notebook in your browser, editing, inserting or deleting cells as desired.
- Changes you make to the notebook will last no longer than your colab or kaggle session.
Install Python package
If you wish to use our programs, perhaps without developing them further, run the command pip install tiatoolbox or pip install --ignore-installed --upgrade tiatoolbox to upgrade from an existing installation.
Detailed installation instructions can be found in the documentation.
To understand better how the programs work, study the jupyter notebooks referred to under the heading Examples Taster.
Command Line
tiatoolbox supports various features through command line. For more information, please try tiatoolbox --help
Prepare for development
Prepare a computer as a convenient platform for further development of the Python package tiatoolbox and related programs as follows.
- Install pre-requisite software
- Open a terminal window
sh
$ cd <future-home-of-tiatoolbox-directory>
- Download a complete copy of the
tiatoolbox.
sh
$ git clone https://github.com/TissueImageAnalytics/tiatoolbox.git
- Change directory to
tiatoolbox
sh
$ cd tiatoolbox
- Create virtual environment for TIAToolbox using
sh
$ conda create -n tiatoolbox-dev python=3.9 # select version of your choice
$ conda activate tiatoolbox-dev
$ pip install -r requirements/requirements_dev.txt
or
sh
$ conda env create -f requirements/requirements.dev.conda.yml # for linux/mac only.
$ conda activate tiatoolbox-dev
- To use the packages installed in the environment, run the command:
sh
$ conda activate tiatoolbox-dev
License
The source code TIAToolbox (tiatoolbox) as hosted on GitHub is released under the BSD-3-Clause license. The full text of the licence is included in LICENSE.
Models weights are dependent on the datasets that they were trained on. Please refer to the documentation for more details.
Cite this repository
If you find TIAToolbox useful or use it in your research, please consider citing our paper:
@article{
Pocock2022,
author = {Pocock, Johnathan and Graham, Simon and Vu, Quoc Dang and Jahanifar, Mostafa and Deshpande, Srijay and Hadjigeorghiou, Giorgos and Shephard, Adam and Bashir, Raja Muhammad Saad and Bilal, Mohsin and Lu, Wenqi and Epstein, David and Minhas, Fayyaz and Rajpoot, Nasir M and Raza, Shan E Ahmed},
doi = {10.1038/s43856-022-00186-5},
issn = {2730-664X},
journal = {Communications Medicine},
month = {sep},
number = {1},
pages = {120},
publisher = {Springer US},
title = {{TIAToolbox as an end-to-end library for advanced tissue image analytics}},
url = {https://www.nature.com/articles/s43856-022-00186-5},
volume = {2},
year = {2022}
}
Owner
- Name: Tissue Image Analytics (TIA) Centre
- Login: TissueImageAnalytics
- Kind: organization
- Location: University of Warwick
- Website: https://warwick.ac.uk/tia/
- Twitter: TIAwarwick
- Repositories: 4
- Profile: https://github.com/TissueImageAnalytics
From tissue images to insights
GitHub Events
Total
- Create event: 42
- Release event: 1
- Issues event: 39
- Watch event: 72
- Delete event: 43
- Member event: 5
- Issue comment event: 129
- Push event: 539
- Pull request event: 89
- Pull request review event: 215
- Pull request review comment event: 164
- Fork event: 16
Last Year
- Create event: 42
- Release event: 1
- Issues event: 39
- Watch event: 72
- Delete event: 43
- Member event: 5
- Issue comment event: 129
- Push event: 539
- Pull request event: 89
- Pull request review event: 215
- Pull request review comment event: 164
- Fork event: 16
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Shan E Ahmed Raza | 1****d | 220 |
| John Pocock | J****P | 101 |
| Shan E Ahmed Raza | s****d@g****m | 67 |
| pre-commit-ci[bot] | 6****] | 25 |
| Mostafa Jahanifar | 7****r | 21 |
| Mark Eastwood | 2****y | 20 |
| DavidBAEpstein | D****n@w****k | 16 |
| John Pocock | j****k@w****k | 15 |
| Ruqayya Awan | 1****a | 13 |
| vqdang | d****3@g****m | 13 |
| Srijay | 5****b | 11 |
| Dmitry Blaginin | d****n@g****m | 11 |
| Simon Graham | s****m@h****k | 10 |
| vqdang | 2****g | 10 |
| adamshephard | 3****d | 9 |
| Simon Graham | 2****m | 6 |
| shaneahmed | sa | 6 |
| Jiaqi-Lv | 6****v | 4 |
| DeepSource Bot | b****t@d****o | 4 |
| Saad Bashir | s****r@h****m | 3 |
| TIA Lab | 6****b | 3 |
| Abdol | a@f****m | 2 |
| Abishek | a****7@g****m | 2 |
| George Hadjigeorgiou | g****7@g****m | 2 |
| wenqi006 | 5****6 | 2 |
| Rob Jewsbury | 3****6 | 1 |
| dependabot[bot] | 4****] | 1 |
| Mark Eastwood | m****7@h****m | 1 |
| Roger Trullo | r****o@h****m | 1 |
| Sarthak Pati | s****i@p****u | 1 |
| and 1 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 78
- Total pull requests: 356
- Average time to close issues: 3 months
- Average time to close pull requests: 17 days
- Total issue authors: 52
- Total pull request authors: 20
- Average comments per issue: 2.36
- Average comments per pull request: 1.63
- Merged pull requests: 307
- Bot issues: 0
- Bot pull requests: 66
Past Year
- Issues: 11
- Pull requests: 39
- Average time to close issues: 28 days
- Average time to close pull requests: 22 days
- Issue authors: 11
- Pull request authors: 9
- Average comments per issue: 0.91
- Average comments per pull request: 1.21
- Merged pull requests: 25
- Bot issues: 0
- Bot pull requests: 9
Top Authors
Issue Authors
- GeorgeBatch (7)
- shaneahmed (6)
- blaginin (4)
- John-P (4)
- mostafajahanifar (3)
- measty (3)
- mrahimpour (2)
- Czzh1 (2)
- KenAncheta (2)
- Himanshunitrr (2)
- FabianHoerst (2)
- Jiaqi-Lv (2)
- sm-ak-r33 (2)
- alevangel (2)
- deeplearningmaniac (2)
Pull Request Authors
- shaneahmed (180)
- pre-commit-ci[bot] (74)
- measty (34)
- Jiaqi-Lv (29)
- blaginin (14)
- John-P (12)
- Abdol (7)
- adamshephard (6)
- mostafajahanifar (5)
- GeorgeBatch (5)
- AbishekRajVG (4)
- ruqayya (3)
- aacic (3)
- moodyhunter (2)
- YijieZhu15 (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 4,813 last-month
- Total docker downloads: 66
-
Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 31
- Total maintainers: 2
pypi.org: tiatoolbox
Computational pathology toolbox developed by TIA Centre.
- Homepage: https://github.com/TissueImageAnalytics/tiatoolbox
- Documentation: https://tiatoolbox.readthedocs.io/
- License: other
-
Latest release: 1.6.0
published about 1 year ago
Rankings
Maintainers (2)
conda-forge.org: tiatoolbox
- Homepage: https://github.com/TissueImageAnalytics/tiatoolbox
- License: BSD-3-Clause
-
Latest release: 1.3.0
published over 3 years ago
Rankings
Dependencies
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