harpy.tb.add_regionprops

harpy.tb.add_regionprops#

harpy.tb.add_regionprops(sdata, labels_name, table_name, output_table_name, properties=('area', 'eccentricity', 'major_axis_length', 'minor_axis_length', 'perimeter', 'centroid', 'convex_area', 'equivalent_diameter', 'major_minor_axis_ratio', 'perim_square_over_area', 'major_axis_equiv_diam_ratio', 'convex_hull_resid', 'centroid_dif'), overwrite=False)#

Calculates region property features from the specified labels element, and adds the results to the AnnData object that annotates the labels element.

This function computes various geometric and morphological properties for each instance found in the specified labels element of the SpatialData object. These properties include the following measures:

  • area

  • eccentricity

  • major_axis_length

  • minor_axis_length

  • perimeter

  • centroid

  • convex_area

  • equivalent_diameter

  • major_minor_axis_ratio

  • perim_square_over_area

  • major_axis_equiv_diam_ratio

  • convex_hull_resid

  • centroid_dif

These features are added to the .obs attribute of the anndata.AnnData table at slot output_table_name.

Note that calculation of perimeter and perim_square_over_area is not supported for 3D labels elements.

Parameters:

  • sdata (SpatialData) – The SpatialData object.

  • labels_name (str | list[str]) – The name of the labels element in sdata that contains the labeled regions, typically derived from a segmentation process. Each distinct label corresponds to a different instance, and properties will be calculated for these labeled regions.

  • table_name (str) – The table element in sdata.tables that annotates the labels element, and to which the calculated features will be added.

  • output_table_name (str) – Output table element.

  • properties (str | tuple[str] (default: ('area', 'eccentricity', 'major_axis_length', 'minor_axis_length', 'perimeter', 'centroid', 'convex_area', 'equivalent_diameter', 'major_minor_axis_ratio', 'perim_square_over_area', 'major_axis_equiv_diam_ratio', 'convex_hull_resid', 'centroid_dif'))) – The properties to calculate.

  • overwrite (bool (default: False)) – If True, overwrites the output element if it already exists in sdata.

Returns:

: The updated sdata object.

Notes

The function operates by pulling the required labels elements (masks) into memory for processing, as the underlying :func:’skimage.measure.regionprops’ functionality does not support lazy loading. Consequently, sufficient memory must be available for large datasets.

Example

import harpy as hp

sdata = hp.datasets.pixie_example()

sdata = hp.tb.allocate_intensity(
    sdata,
    image_name="raw_image_fov0",
    labels_name="label_whole_fov0",
    to_coordinate_system="fov0",
    mode="sum",
    output_table_name="table_intensities",
    overwrite=True,
)

sdata = hp.tb.allocate_intensity(
    sdata,
    image_name="raw_image_fov1",
    labels_name="label_whole_fov1",
    to_coordinate_system="fov1",
    mode="sum",
    output_table_name="table_intensities",
    append=True,
    overwrite=True,
)

sdata = hp.tb.add_regionprops(
    sdata,
    labels_name=["label_whole_fov0", "label_whole_fov1"],
    table_name="table_intensities",
    output_table_name="table_intensities",
    properties=["perimeter", "equivalent_diameter"],
    overwrite=True,
)