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@tulerpetontidae tulerpetontidae commented Jul 19, 2022

The current implementation of feature calculation is extremely slow (takes more time than the segmentation itself for large images). I suggest speeding it up using sparse matrices.

  • Post hoc feature calculation on the whole image (FastNucleiFeatures class)
  • Add option for sparse matrix storage (convenient for downstream analysis)
  • Try to speed up build in NucleiFeatures class. It should be less memory intense but might not add that much speed at the end
  • Change example notebook

Happy to hear your suggestions @yozhikoff

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