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 #376
• @VarunUllanat made their first contribution in #378

Full Changelog: v2.1.1...v3.0.0

What's Changed

• use current year in docs by @jacob-rosenthal in #311
• pin protobuf to 3.20.1 by @jacob-rosenthal in #314
• Make error message for extract_region more informative by @jacob-rosenthal in #320
• Add action to enforce pre-commit hooks by @tddough98 in #333
• Merge main branch into dev by @tddough98 in #334
• Bump ipython from 7.31.1 to 8.10.0 in /docs by @dependabot in #346
• Fixed docs by @sreekarreddydfci in #348

New Contributors

• @tddough98 made their first contribution in #333

Full Changelog: v2.1.0...v2.1.1

What's Changed

• Clean SegmentMIF by @ryanccarelli in #294
  • Removed GPU argument from SegmentMIF
  • Separated whole_cell and nuclear kwargs
• Update README.md by @surya-narayanan in #298
• Update quantify mif by @jacob-rosenthal in #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 #306
  • Fixed bug for generate_tiles() within OpenSlideBackend and BioFormatsBackend. Tile shape evenly divides into slide shape
• Added logging functionality by @BeeGass in #304
  • Includes logger customization
• Don't augment test or valid splits for PanNuke by @jacob-rosenthal in #309

New Contributors

• @BeeGass made their first contribution in #304

Full Changelog: 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 #275
• @Yu-AnChen made their first contribution in #287

Full Changelog: v2.0.3...v2.0.4

What's Changed

• Fix bug in BioFormats backend #272

Full Changelog: 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: v2.0.1...v2.0.2

Test release to debug dockerization GitHub Actions workflow

#245 #145

Test release to debug dockerization GitHub Actions workflow

#245 #145

Test release to debug dockerization GitHub Actions workflow

#245 #145

Test release to check that dockerization GitHub Actions workflow is working properly

#245 #145