Code

Expand cellpose options#650

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Merged

jluethi merged 26 commits intomainfractal-analytics-platform/fractal-tasks-core:mainfrom 649-cellpose-optionsfractal-analytics-platform/fractal-tasks-core:649-cellpose-optionsCopy head branch name to clipboardFeb 15, 2024

+747-7

Commits

Commits on Jan 31, 2024

• Add Cellpose options

  jluethi

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  6047284

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• Switch to using Enums for model_type in Cellpose task

  jluethi

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  3ce46eb

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• Update changelog

  jluethi

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  1e05b8f

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• Update manifest

  jluethi

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  12064ac

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• bump version to 0.14.2a0

  jluethi

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  281f9b2

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• Fix check in cellpose task pretrained_model path validation

  jluethi

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  33e0472

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• Update tests for cellpose task with new model_type input validation

  jluethi

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• Add a comment on potential test failure due to cellpose updates to cellpose tests

  jluethi

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  e6c0b65

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• Bump version to 0.14.2a1

  jluethi

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Commits on Feb 6, 2024

• Add a CellposeCustomNormalizer model and implement custom image normalization for the Cellpose task

  jluethi

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  ec12e90

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• Update Changelog

  jluethi

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Commits on Feb 7, 2024

• Update manifest creation to include CellposeCustomNormalizer model

  jluethi

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Commits on Feb 8, 2024

• Do not construct CellposeCustomNormalizer from within function-argument default value

  tcompa

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  a9185ba

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• Fix using the correct normalize call to model.eval

  jluethi

  committed
  4d6099f

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• Merge branch '649-cellpose-options' of https://github.com/fractal-analytics-platform/fractal-tasks-core into 649-cellpose-options

  jluethi

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  13342bd

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• Add constraints for percentiles

  jluethi

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  f3b38ff

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• Add test for CellposeCustomNormalizer

  jluethi

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  58f974c

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• Increase version to 0.14.2a2

  jluethi

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  061c5ce

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• Remove clipping from normalization with bounds

  jluethi

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  46bfa0b

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• Add tests for normalized_img

  jluethi

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  25aecf9

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Commits on Feb 15, 2024

• Update Cellpose normalization pydantic model

  jluethi

  committed
  66a5218

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• Switch to Option 3: Provide CellposeCustomNormalizer() as default value for normalize

  jluethi

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  e62c7fe

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• Improve CellposeCustomNormalizer: make type required

  jluethi

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  cd6f134

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• Docstrings & cleanups

  jluethi

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  15a0894

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• Revert manual version updates

  jluethi

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  0085a13

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• Add type hint of helper function

  jluethi

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  e7c1d74

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