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Stain Normalization with Macenko's method #394

Merged
merged 19 commits into from Jan 14, 2023
Merged

Stain Normalization with Macenko's method #394

merged 19 commits into from Jan 14, 2023

Commits on Jan 14, 2023

  1. Refactor and fix RGB to OD filter to return float np.array instead of… 

    … PIL Image
    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  2. Correct formula for RGB to OD conversion and don't rescale intensity

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  3. Don't blend alpha channel but just remove it

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  4. Add LinalgMixin with method

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  5. Background intensity as a parameter

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  6. Calculate two principal components with eigenvectors decomposition

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  7. Add Stain Normalizer with Macenko's method

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  8. Add TransformerStainMatrixMixin

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  9. Add some unit tests for TransformerStainMatrixMixin

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  10. Fix mock bug under py 3.6 

    https://bugs.python.org/issue23078
    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  11. Complete unit tests

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  12. Add integration tests

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  13. Add copyright

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  14. Add stain_normalizer API docs page

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  15. Docstrings and variables naming improvements per comments

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  16. Move new files in correct folder

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  17. fixed tests for stain normalization for new skimage version

    @nicolebussola @alessiamarcolini
    nicolebussola authored and alessiamarcolini committed Jan 14, 2023
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  18. Fix incorrect assertion

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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  19. Generalize calculation of principal components

    @alessiamarcolini
    alessiamarcolini committed Jan 14, 2023
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