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mahmoodlab / CLAM

Open source tools for computational pathology - Nature BME
http://clam.mahmoodlab.org
GNU General Public License v3.0
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Black foreground after `segment` and pixel garbled after `stitch` #98

Closed pzSuen closed 2 years ago

pzSuen commented 2 years ago

I am trying to use the original code and parameters to preprocess the slides in CAMELYON17, but I encounter this problem as seen in the picture.

As you can see, the first problem is that the tissue in the bottom of the segment mask is grey with a green segment boundary. The second problem is garbled after stitching, I don't know whether the pixel will be garbled when I compute the features.

image

Thank you very much!

fedshyvana commented 2 years ago

it's a pixman issue - try installing pixman 0.40 (https://anaconda.org/anaconda/pixman)

pzSuen commented 2 years ago

The problem is solved. Thank you very much!