Recent Releases of pathml
pathml -
What's Changed
- Torch Dependency: Updated Torch dependency to 2.6.0. Change was needed due to security issues with the older versions of Torch. Torch 2.6.0 only works on Python >= 3.9. 2.
- Python
Published by jamesgwen 10 months ago
pathml - v3.0.0
What's Changed
- Graph API Integration: Added a comprehensive graph API with supporting codebase, tests, and notebooks, enabling advanced graph-based analyses.
- Tile-Stitching Capabilities: Introduced sophisticated tile-stitching functionality with refactored code and test cases for improved image handling and analysis.
- ONNX-Based Inference Support: Enabled ONNX-based inference workflows, boosting model inference efficiency and compatibility.
- Expanded Testing and Documentation: Added extensive test cases, updated example notebooks, refined README, and enhanced documentation for improved usability.
- Workflow Enhancements: Introduced manual workflow triggers, support for Windows testing, and workflow integration for Vectra slide processing.
New Contributors
- @Dana-Farber made their first contribution in https://github.com/Dana-Farber-AIOS/pathml/pull/376
- @VarunUllanat made their first contribution in https://github.com/Dana-Farber-AIOS/pathml/pull/378
Full Changelog: https://github.com/Dana-Farber-AIOS/pathml/compare/v2.1.1...v3.0.0
- Python
Published by VarunUllanat over 1 year ago
pathml - v2.1.1
What's Changed
- use current year in docs by @jacob-rosenthal in https://github.com/Dana-Farber-AIOS/pathml/pull/311
- pin protobuf to 3.20.1 by @jacob-rosenthal in https://github.com/Dana-Farber-AIOS/pathml/pull/314
- Make error message for extract_region more informative by @jacob-rosenthal in https://github.com/Dana-Farber-AIOS/pathml/pull/320
- Add action to enforce pre-commit hooks by @tddough98 in https://github.com/Dana-Farber-AIOS/pathml/pull/333
- Merge main branch into dev by @tddough98 in https://github.com/Dana-Farber-AIOS/pathml/pull/334
- Bump ipython from 7.31.1 to 8.10.0 in /docs by @dependabot in https://github.com/Dana-Farber-AIOS/pathml/pull/346
- Fixed docs by @sreekarreddydfci in https://github.com/Dana-Farber-AIOS/pathml/pull/348
New Contributors
- @tddough98 made their first contribution in https://github.com/Dana-Farber-AIOS/pathml/pull/333
Full Changelog: https://github.com/Dana-Farber-AIOS/pathml/compare/v2.1.0...v2.1.1
- Python
Published by sreekarreddydfci almost 3 years ago
pathml - 2.1.0
What's Changed
- Clean SegmentMIF by @ryanccarelli in https://github.com/Dana-Farber-AIOS/pathml/pull/294
- Removed GPU argument from SegmentMIF
- Separated whole_cell and nuclear kwargs
- Update README.md by @surya-narayanan in https://github.com/Dana-Farber-AIOS/pathml/pull/298
- Update quantify mif by @jacob-rosenthal in https://github.com/Dana-Farber-AIOS/pathml/pull/301
- update the functional implementation F() to not require a tile object.
- Add "label" property to counts matrix.
- Fix tiling bug by @jacob-rosenthal in https://github.com/Dana-Farber-AIOS/pathml/pull/306
- Fixed bug for
generate_tiles()withinOpenSlideBackendandBioFormatsBackend. Tile shape evenly divides into slide shape
- Fixed bug for
- Added logging functionality by @BeeGass in https://github.com/Dana-Farber-AIOS/pathml/pull/304
- Includes logger customization
- Don't augment test or valid splits for PanNuke by @jacob-rosenthal in https://github.com/Dana-Farber-AIOS/pathml/pull/309
New Contributors
- @BeeGass made their first contribution in https://github.com/Dana-Farber-AIOS/pathml/pull/304
Full Changelog: https://github.com/Dana-Farber-AIOS/pathml/compare/v2.0.4...v2.1.0
- Python
Published by BeeGass almost 4 years ago
pathml - v2.0.4
What's Changed
- Fix bug caused by mixing up (i, j) and (x, y) coordinate systems in BioFormatsBackend (#278)
- Add option to not normalize image in
BioFormatsBackend.extract_region()(#279) - Fix logic when inferring correct backend to use from file path which was failing on paths containing periods (#284)
- Fix bug to correctly pass
image_resolutionargument to Mesmer model (#286) - Fix outdated url for PanNuke dataset (#287) by @Yu-AnChen
- Fix GitHub Actions configuration which was causing testing suite to hang (#289)
New Contributors
- @dependabot made their first contribution in https://github.com/Dana-Farber-AIOS/pathml/pull/275
- @Yu-AnChen made their first contribution in https://github.com/Dana-Farber-AIOS/pathml/pull/287
Full Changelog: https://github.com/Dana-Farber-AIOS/pathml/compare/v2.0.3...v2.0.4
- Python
Published by jacob-rosenthal about 4 years ago
pathml - v2.0.2
What's Changed
- Streamline environment setup by removing spams as a dependency (#142) and updating
environment.ymlto create an environment with both PathML and deepcell (#259 #210) - Add a Dockerfile for another installation option, and a GitHub Actions workflow to build and publish it to Dockerhub on new release (#145)
- Add
series_as_channelsflag toBioFormatsBackend.extract_region()to fix support for images from the MISI lab (#261)
Full Changelog: https://github.com/Dana-Farber-AIOS/pathml/compare/v2.0.1...v2.0.2
- Python
Published by jacob-rosenthal about 4 years ago
pathml - v2.0.0
What's new in v2.0.0:
- Changed h5path format and refactored h5manager to improve performance (#231)
- support XYZCT images for TileDataset (#233)
- Cleaned up versioning tracker (#236)
- fix bug when reading region from openslide backend at higher levels (#242)
- Add support for multi-series images with BioformatsBackend (#251)
- Pin python-bioformats version to avoid any possibility of log4j hacks (#256)
- Added optional flag in
SlideDataset.run()to write slides to h5path as they finish processing (#226) - Added GitHub Actions workflow to automatically build package and publish to PyPI when a new release is created (#235)
Because the file format is changed in this version, .h5path files saved in older versions will not be able to be loaded in this one, and vice versa (i.e. breaking backwards compatibility, hence the bumped major version).
- Python
Published by jacob-rosenthal about 4 years ago