scverse/napari-spatialdata

Bug with contrast limit calculation for multiscale images

LucaMarconato opened this issue · 0 comments

The code changes added here regarding the contrast limit adjustment: d639dd7
lead to an error when changing channel for a multiscale multichannel image. This can be reproduced with morphology_focus from this Xenium Multimodal Segmentation dataset: https://github.com/giovp/spatialdata-sandbox/tree/main/xenium_2.0.0_io.

I discussed this with @melonora, we would need to:

  • fix the how the contrast limit is computed in _view.py
  • preferably add a comment in _view.py in which has_anndata is used (because an AnnData object that shows the channel names on the View widget is added).