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Merging from dev_graph#9

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sreekarreddydfci merged 48 commits intodev-crossplatformtestssreekarreddydfci/pathml:dev-crossplatformtestsfrom dev-tilestitchingsreekarreddydfci/pathml:dev-tilestitchingCopy head branch name to clipboardMar 5, 2024

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Commits

Commits on Feb 6, 2024

• Make pre-commit compliant

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• Update tests-conda.yml

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• Update tests-conda.yml

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• revert back to old environment

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• Merge branch 'dev_graph' of https://github.com/Dana-Farber-AIOS/pathml into dev_graph

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• Update tests-conda.yml to remove Deepcell install

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• Update tests-conda.yml to free space

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Commits on Feb 7, 2024

• Merge pull request Dana-Farber-AIOS#417 from sreekarreddydfci/dev-tilestitching

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• Merge remote-tracking branch 'upstream/dev_graph' into dev-tilestitching

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• Merge pull request Dana-Farber-AIOS#418 from Dana-Farber-AIOS/dev-tilestitching

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Commits on Feb 8, 2024

• Added new two-hop computation

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• Merge branch 'dev_graph' of https://github.com/Dana-Farber-AIOS/pathml into dev_graph

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• Added python version in environment file

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• Removed deepcell installation

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Commits on Feb 9, 2024

• Updated graph utils and clean

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Commits on Feb 15, 2024

• Update test_inference.py

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• Update test_inference.py

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Commits on Feb 21, 2024

• Updated stain normalization class

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• Updated stain normalization class

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• `Merge branch 'dev_graph' of https://github.com/Dana-Farber-AIOS/pathml into dev_graph

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• Updated graph utils tests

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Commits on Feb 22, 2024

• Updated example notebooks

  sreekarreddydfci

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• Merge remote-tracking branch 'upstream/dev_graph' into dev-tilestitching

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• Updated graphs notebook

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• Added documentation for graph API

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• Merge pull request Dana-Farber-AIOS#419 from sreekarreddydfci/dev-tilestitching

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• Merge pull request Dana-Farber-AIOS#420 from Dana-Farber-AIOS/dev-tilestitching

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Commits on Feb 23, 2024

• Updated environment file, added instructions and references

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• Cleaned up examples and setup.py

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Commits on Feb 26, 2024

• Updated example notebook

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• Updated notebooks and docs

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• Updated notebooks and docs

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• Added JCO example

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• Added JCO example

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Commits on Feb 27, 2024

• Reformatted README installation instructions

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• Update README.md

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Commits on Feb 28, 2024

• Update README.md

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• Update README.md

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• Update setup.py to add torch cuda installation

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• Update README.md

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• Added comments for stain normalization

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Commits on Mar 1, 2024

• Added our implementation of mesmer model

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Commits on Mar 4, 2024

• Adding note on where mesmer output is saved to doc string

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• Adjusting the header in mesmer utils file to contain citation

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• Added betters tests for segmentmif

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• Added no coverage comments

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Commits on Mar 5, 2024

• Merging changes from dev_graph

  sreekarreddydfci

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• Merge branch 'dev-crossplatformtests' into dev-tilestitching

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