fishtank.seg.masks_to_polygons

fishtank.seg.masks_to_polygons#

fishtank.seg.masks_to_polygons(masks, tolerance=0.5, id='cell', z='z')#

Covert segmentation masks to polygons.

Parameters:

  • masks (ndarray) – a (Y,X) or (Z,Y,X) numpy array of segmentation masks.

  • tolerance (float (default: 0.5)) – The maximum allowed geometry displacement. The higher this value, the smaller the number of vertices in the resulting geometry.

  • id (str (default: 'cell')) – The name of the id column in the resulting GeoDataFrame

  • z (str (default: 'z')) – The name of the z column in the resulting GeoDataFrame

Return type:

GeoDataFrame

Returns:

polygons a GeoDataFrame of cell outlines.

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