Pathml

What's Changed
1. **Graph API Integration**: Added a comprehensive graph API with supporting codebase, tests, and notebooks, enabling advanced graph-based analyses.
2. **Tile-Stitching Capabilities**: Introduced sophisticated tile-stitching functionality with refactored code and test cases for improved image handling and analysis.
3. **ONNX-Based Inference Support**: Enabled ONNX-based inference workflows, boosting model inference efficiency and compatibility.
4. **Expanded Testing and Documentation**: Added extensive test cases, updated example notebooks, refined README, and enhanced documentation for improved usability.
5. **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

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

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()` within `OpenSlideBackend` and `BioFormatsBackend`. Tile shape evenly divides into slide shape
* 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

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_resolution` argument 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

What's Changed
* Fix bug in BioFormats backend 272

**Full Changelog**: https://github.com/Dana-Farber-AIOS/pathml/compare/v2.0.2...v2.0.3

What's Changed
* Streamline environment setup by removing spams as a dependency (142) and updating `environment.yml` to 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_channels` flag to `BioFormatsBackend.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