fishtank.seg.assign_spots#
- fishtank.seg.assign_spots(spots, polygons, max_dist=5, cell='cell', x='global_x', y='global_y', z=None, polygons_z=None, fov=None)#
Assigns spots to the nearest polygon
- Parameters:
spots (
DataFrame) – a DataFrame of spot coordinates. Can be 2D or 3D.polygons (
GeoDataFrame) – a GeoDataFrame of cell outlines. Can be 2D or 3D.max_dist (
float|int(default:5)) – the maximum distance to search for the nearest polygon.cell (
str(default:'cell')) – the name of the cell column in the polygons.x (
str(default:'global_x')) – the name of the x column in the spots.y (
str(default:'global_y')) – the name of the y column in the spots.z (
Optional[str] (default:None)) – the name of the z column in the spots. If None, the polygons are assumed to be 2D.polygons_z (
Optional[str] (default:None)) – the name of the z column in the polygons. If None, the spots z values will be used.fov (
Optional[str] (default:None)) – the name of the fov column in the spots. If None, will do global alignment.
- Return type:
DataFrame- Returns:
spots the spots DataFrame with
{cell}and{cell}_distcolumns added.