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Feature extraction from GEOJson nuclei and tissue segmentation maps

Home Page: https://okunator.github.io/cellseg_gsontools/

License: MIT License

Python 100.00%
clustering-methods digital-pathology feature-extraction graph-algorithms immune-infiltration morphological-analysis nuclei-segmentation regionalization roi-selection spatial-data-analysis tissue-segmentation whole-slide-annotation whole-slide-image

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weights2gdf not working

I have segmented a WSI and extracted a 512x512 patch from it by hap_cells = cells.cx[x:x+512, y:y+512].

image

image

Following the user guide "Cell/Nuclei Neighborhood Distances and Characteristics", I would like to fit a connectivity graph to the resulting 157 cells. When executing w = fit_graph(hap_cells, type="delaunay", thresh=200, id_col="uid") I get many warnings like this:

  1. passing a BlockManager to GeoDataFrame is deprecated and will be removed in a future version. Use public APIs instead.
  2. the geometry is in a geographic CRS. The results of 'centroid' are probably wrong. Use 'GeoSeries.to_crs()' to reproject geometries to a projected CRS before this operation.
    image

When running wdf = weights2gdf(hap_cells, w) I get an error:

TypeError: sequence item 0: expected str instance, NoneType found

image

What could be the reason for this and what have I done wrong? Can you help me?

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