smurf.spatial_object.spatial_object.generate_cell_spots_information

spatial_object.generate_cell_spots_information(max_spot=50, cells_main_pct=0.16666666666666666)

Generates cells and spots information and creates a nearest neighbor network.

This method processes the segmentation data to extract cell and spot information. It filters cells based on specified criteria and constructs a k-nearest neighbors (kNN) network.

Parameters:

  • max_spot (int, optional) – The maximum number of spots per cell to consider. Defaults to 50.

  • cells_main_pct (float, optional) – The minimum percentage of a cell that must be present in a spot to be considered. Defaults to 1/6.

Returns:

None. The method updates the spatial object attributes with cells, spots, and network information.

Return type:

None