Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
OpenSlide Patch Manager
Basic Info
Statistics
- Stars: 4
- Watchers: 2
- Forks: 6
- Open Issues: 3
- Releases: 0
Topics
Metadata Files
README.md
OPM
THIS CODE IS NOW DEPRECATED IN FAVOR OF github.com/mlcommons/GaNDLF
Open Patch Manager: parallel reading/writing of patches.
Installation:
For Usage Only
```powershell conda create -p ./venv python=3.8.12 -y conda activate ./venv pip install OpenPatchMiner
alternate
conda install -c conda-forge openpatchminer
```
For OPM Development
powershell
git clone https://github.com/CBICA/OPM.git
cd OPM/
conda create -p ./venv python=3.8.12 -y
conda activate ./venv
pip install .
Usage
To try an example: ```powershell
continue from virtual environment shell
Extract 10 tissue patches from images/example_slide.tiff
python patchminer.py -i images/exampleslide.tiff -lm images/example_lm.tiff -o example -c opm/config.yml
Use the output manifest from last run (example/list.csv) to re-extract the same patches for a different replicate
This is useful if you have multiple slides/label maps and you want corresponding coordinates from each of them
python patchminer.py -i images/exampleslide.tiff -lm images/examplelm.tiff -c opm/config.yml -o examplereplicate --input_csv example/list.csv ``` By default it detects tissue and extracts 1000 random patches from the included .svs file. Play with this number as well as the number of parallel threads in example.py (default patches=1000, default threads=100)
Options
There are also a handful of useful options:
- READ_TYPE: either 'sequential' or 'random'. If sequential, it repeatedly takes the top-leftmost valid index until quota is met or the slide is saturated. If random, it randomly samples a patch from the valid indices until saturated or the quota is hit.
... and various other parameters such as patch size, thumbnail/valid mask scale, and masking thresholds.
Workflow
OPM follows the following workflow:
Project Structure
.
├── images
│ ├── example_lm.tiff
│ ├── example_slide.tiff
│ └── opm_flowchart.png
├── LICENSE.txt
├── opm
│ ├── config.py
│ ├── __init__.py
│ ├── patch_manager.py
│ ├── patch.py
│ └── utils.py
├── patch_miner.py
├── README.md
├── setup.cfg
└── setup.py
Changelog
Dec. 14, 2021: - Replaced slide library with tifffile - Made barebones OpenSlide mimic with tifffile, named SlideObject - Updated requirements, bumped minimum python from 3.6 --> 3.8 (due to zarr requirements) - Updated README
Dec. 9, 2021: - Changed backend to Pandas. - Updated README
Nov. 17, 2020: - Added support for mining patches from label map along with the slide. - Updated README
Jul. 31, 2020:
- Changed ALLOW_OVERLAP to OVERLAP_FACTOR. OVERLAP_FACTOR is a float from 0 to 1 that is the portion of patches that are allowed to overlap. If 0, there is no overlap allowed. If 1, they are totally allowed to overlap (except for the origin pixel).
Owner
- Name: Center for Biomedical Image Computing & Analytics (CBICA)
- Login: CBICA
- Kind: organization
- Email: software@cbica.upenn.edu
- Location: Philadelphia, PA
- Website: https://www.med.upenn.edu/cbica/
- Twitter: CBICAannounce
- Repositories: 21
- Profile: https://github.com/CBICA
CBICA focuses on the development and application of advanced computation techniques.
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| sarthakpati | s****i@h****m | 106 |
| grenkoca | g****a@g****m | 54 |
| Caleb Grenko | 3****a@u****m | 46 |
| Sarthak Pati | s****i@p****u | 4 |
| dependabot[bot] | 4****]@u****m | 1 |
| geeks-sid | s****r@g****m | 1 |
| Jose L. Agraz, PhD | j****1@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 8
- Total pull requests: 30
- Average time to close issues: 3 months
- Average time to close pull requests: 9 days
- Total issue authors: 2
- Total pull request authors: 5
- Average comments per issue: 1.13
- Average comments per pull request: 0.7
- Merged pull requests: 26
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- sarthakpati (7)
- katesedykh (1)
Pull Request Authors
- sarthakpati (18)
- grenkoca (8)
- Geeks-Sid (2)
- shubhaminnani (1)
- joseagraz (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 329 last-month
-
Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 14
- Total maintainers: 1
pypi.org: openpatchminer
A patch miner for large histopathology images
- Homepage: https://github.com/CBICA/OPM
- Documentation: https://openpatchminer.readthedocs.io/
- License: BSD-3-Clause License
-
Latest release: 0.1.8
published over 3 years ago
Rankings
Maintainers (1)
conda-forge.org: openpatchminer
- Homepage: https://github.com/CBICA/OPM
- License: BSD-3-Clause
-
Latest release: 0.1.8
published over 3 years ago