[grlee77]

This MR impelements four colocaliziation measures being introduced for scikit-image 0.20. The implementation of each is fairly simple. For reference, see a related gallery example.

Benchmark results vs. scikit-image 0.20dev

Benchmark results show speedup in all cases below aside from intersection_coeff on small images.

function	shape	dtype	acceleration
manders_coloc_coeff	(512, 512)	float32	1.72
manders_coloc_coeff	(512, 512)	uint8	2.93
manders_coloc_coeff	(3840, 2160)	float32	39.3
manders_coloc_coeff	(3840, 2160)	uint8	49.9
manders_coloc_coeff	(192,192,192)	float32	38.1
manders_coloc_coeff	(192,192,192)	uint8	47.4

function	shape	dtype	acceleration
manders_overlap_coeff	(512, 512)	float32	1.41
manders_overlap_coeff	(512, 512)	uint8	1.48
manders_overlap_coeff	(3840, 2160)	float32	2.33
manders_overlap_coeff	(3840, 2160)	uint8	2.93
manders_overlap_coeff	(192,192,192)	float32	2.31
manders_overlap_coeff	(192,192,192)	uint8	2.80

function	shape	dtype	acceleration
pearson_corr_coeff	(512, 512)	float32	6.96
pearson_corr_coeff	(512, 512)	uint8	8.10
pearson_corr_coeff	(3840, 2160)	float32	49.5
pearson_corr_coeff	(3840, 2160)	uint8	53.4
pearson_corr_coeff	(192,192,192)	float32	51.6
pearson_corr_coeff	(192,192,192)	uint8	52.5

function	shape	dtype	acceleration
intersection_coeff	(512, 512)	bool	0.278
intersection_coeff	(3840, 2160)	bool	13.1
intersection_coeff	(192,192,192)	bool	11.1

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 88.57143% with 8 lines in your changes missing coverage. Please review.

Project coverage is 92.88%. Comparing base (a8d9690) to head (1fa1633).
Report is 6 commits behind head on branch-23.02.

Files with missing lines	Patch %	Lines
...cucim/src/cucim/skimage/measure/_colocalization.py	86.20%	8 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff                @@
##           branch-23.02     #488      +/-   ##
================================================
- Coverage         92.95%   92.88%   -0.07%     
================================================
  Files               130      131       +1     
  Lines              9775     9890     +115     
================================================
+ Hits               9086     9186     +100     
- Misses              689      704      +15     

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[gigony]

intersection_coeff (512, 512) bool 0.278

I wonder if this result is okay and if you have an idea on what caused the performance degradation.

[gigony]

Thanks @grlee77 ! It looks good to me! (with a minor typo that can be addressed later).

[grlee77]

/merge