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VGeorgii / Microsa

Python library designed for tissue microenvironment spatial analysis
MIT License
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unexpected keyword argument 'neighbors' #1

Closed golnaz-ltri closed 1 year ago

golnaz-ltri commented 1 year ago

Hello, I am trying to replicate the analysis for this package, however when I reach the step for fibers skeletonization and labeling, in the first line of code to define fibre-exe I get a keyword argument error: TypeError: label() got an unexpected keyword argument 'neighbors'

All packages are updated as required.

VGeorgii commented 1 year ago

Hey!

You are probably using the newest version of skimage library. They have changed a couple of functions. Try next thing: go to the microsaa folder > open fibseg file > find to lines with code _skellabels = label(skeleton, neighbors = 8) and _skel_labelspruned = label(pruning, neighbors = 8) > replace the argument neighbors = 8 to connectivity = 2. That should help.

golnaz-ltri commented 1 year ago

Thank you! This fixed the issue.