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Tracking issue for FlowSOM interoperability #6

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berombau opened this issue Mar 12, 2024 · 0 comments
Open
8 tasks

Tracking issue for FlowSOM interoperability #6

berombau opened this issue Mar 12, 2024 · 0 comments
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@berombau
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Clustering with FlowSOM is possible and cell clustering with napari-cluster-plotter (https://github.com/saeyslab/harpy/blob/main/experiments/example_of_cluster_plotter.ipynb) is possible. It would be interesting to view the FlowSOM tree in a similar widget and allow labeling of the metaclusters on the tree (similar to Pixie pipeline notebook GUI, but with the imaging data in napari instead of Mantis).

  • create Widget class
  • button to cluster
  • button to plot FlowSOM tree
  • button to get labels in table
  • select with lasso tool
  • view selection on images
  • allow renaming metacluster labels to cell type names
  • plot cluster heatmap similar to to Pixie pipeline
@berombau berombau self-assigned this Apr 23, 2024
@berombau berombau added this to the Spatial omics conference milestone Apr 23, 2024
@berombau berombau modified the milestones: Release 0.0.3, Release 0.0.2 Aug 12, 2024
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