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saeyslab / napari-sparrow

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problems with contrast enhancing #126

Closed lopollar closed 1 year ago

lopollar commented 1 year ago

The chunking in the CLAHE function really causes problems, even when setting the depth high enough. With a depth of 8192, I still get tiling effects where there were no tiling effects before..

image @ArneDefauw , how did you fix this for the Vizgen datasets, because it is really ugly now in my case...

ArneDefauw commented 1 year ago

should be fixed by https://github.com/saeyslab/napari-sparrow/commit/9df0b9dd4948c54e4a38d09c8edd36fc07214d66 . Seems like a bug in the apply function of squidpy. Now using map_overlap of dask directly.

Tested on complete vizgen image, processed as one slice. Plots of two subsets below:

clahe_

clahe_2