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Defense-Circuits-Lab / findmycells

An end-to-end bioimage analysis pipeline with state-of-the-art tools for non-coding experts
https://defense-circuits-lab.github.io/findmycells/
GNU General Public License v3.0
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set dependencie versions: imageio, scikit-image #5

Closed KonKob closed 1 year ago

KonKob commented 1 year ago

I followed the installation instructions, downloaded the test data and went through the GUI tutorial, but somehow at this step, it fails... User system: MacOS

image image
KonKob commented 1 year ago

SOLUTION: the .imwrite function in imageio, that is used via skimageio was updated in v.2.22 => Downgrade imageio: pip install --upgrade imageio==2.21.3

KonKob commented 1 year ago

For developers: write imageio.v2.imwrite in case the imwrite function is called directly outside skimageio

KonKob commented 1 year ago

There is a second dependency issue with scikit-image. It breaks the shape of the images when saving them (it creates 1024x1px rows for an image of shape (1024x1024)):

image

SOLUTION: pip install scikit-image==0.19.3