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[WIP] Adding Stain Normalization Transform for Pathology#1998

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nsrivathsa wants to merge 36 commits intoProject-MONAI:devfrom
nsrivathsa:neha/stain-norm-2
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[WIP] Adding Stain Normalization Transform for Pathology#1998
nsrivathsa wants to merge 36 commits intoProject-MONAI:devfrom
nsrivathsa:neha/stain-norm-2

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@nsrivathsa nsrivathsa commented Apr 13, 2021 •
edited by bhashemian
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Description

Adds a Transform for CuPy-based Stain Normalization for Pathology.

Status

Work in progress

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

@nsrivathsa
added stain norm and tests
3e2de71 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa nsrivathsa marked this pull request as ready for review April 13, 2021 03:23
@bhashemian bhashemian mentioned this pull request Apr 13, 2021
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@bhashemian bhashemian self-requested a review April 13, 2021 04:01
@bhashemian bhashemian changed the title [WIP] Adding Stain Normalization Transform for Pathology (2) [WIP] Adding Stain Normalization Transform for Pathology Apr 13, 2021
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bhashemian reviewed Apr 14, 2021
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Well done, @nsrivathsa! I left few comments inline.
In general, can you think of edge cases in physical world for test cases as well, like the situation that we expect to have only one stain so the concentration of the other one is zero.
Also it would be great to have input images that are not uniformly filled.
Keep in mind that writing solid unittests are very important to ensure the correctness of our code and it might take more time than implementing the original functions and classes.

@nsrivathsa
import changes
e197f9d 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
changed stain extraction tests
ad957fa 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
edited stain norm tests
00518fa 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
convert floats to float32
45a2ac5 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
added uint8 assumption to docstring
4b0f696 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
add error case
cb99aef 
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa nsrivathsa requested a review from bhashemian April 19, 2021 23:42
bhashemian
bhashemian reviewed Apr 23, 2021
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bhashemian commented Apr 28, 2021

@nsrivathsa I see that lines 47-75 for stain extraction are being repeated in line 143-171 for stain normalization. Can you modify the code so that it reuses stain extraction in stain normalization?

@bhashemian bhashemian force-pushed the neha/stain-norm-2 branch from 5294bf2 to be88f7d Compare May 3, 2021 16:31
@bhashemian bhashemian marked this pull request as draft July 9, 2021 16:30
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madil90 commented Jul 19, 2021

/build

@bhashemian bhashemian mentioned this pull request Jul 28, 2021
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6 tasks
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bhashemian commented Aug 2, 2021

A variant of this PR is merged.

@bhashemian bhashemian closed this Aug 2, 2021
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3 participants

@nsrivathsa @bhashemian @madil90