fishtank.scripts.assign_spots

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fishtank.scripts.assign_spots#

fishtank.scripts.assign_spots(input, polygons='polygons.json', output='assigned_spots.csv', max_dist=0, cell_column='cell', subset=None, x_column='global_x', y_column='global_y', z_column=None, polygons_z_column=None, cell_fill=0, alignment=None, map_z=False, **kwargs)#

Assign spots to the nearest polygon.

fishtank assign-spots -i input -p polygons -o output

Parameters:

  • input (str | Path) – Spots input file path.

  • polygons (str | Path (default: 'polygons.json')) – Polygons input file path.

  • output (str | Path (default: 'assigned_spots.csv')) – Output file path.

  • max_dist (float (default: 0)) – Maximum distance from polygon edge for spot assignment.

  • cell_column (str (default: 'cell')) – Column containing cell ID in polygons.

  • subset (Union[str, Path, None] (default: None)) – Set of polygons to assign spots to.

  • x_column (str (default: 'global_x')) – Column containing x-coordinate in spots.

  • y_column (str (default: 'global_y')) – Column containing y-coordinate in spots.

  • z_column (Optional[str] (default: None)) – Column containing z-slice in spots. None for 2D polygons.

  • polygons_z_column (Optional[str] (default: None)) – Column containing z-slice in polygons. Defaults to z_column.

  • cell_fill (int (default: 0)) – Fill value for unassigned cells.

  • alignment (Union[str, Path, None] (default: None)) – File used to align spots space to polygons space.

  • map_z (bool (default: False)) – Map spot z values to polygon z values.

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