napari_prism.im.measure_tma

napari_prism.im.measure_tma(spatialdata, image_name, segmentation_name, output_table_name, tiling_shapes=None, extended_properties=False, intensity_mode='mean', reference_coordinate_system='global', inplace=True, scale='scale0')

Measures the properties of the labels or cells in the image from a given labels mask. Writes the measurements as an AnnData table to the underlying sdata object.

Parameters:

• spatialdata (SpatialData) – The spatialdata object to measure.

• image_name (str) – The name of the image to measure.

• segmentation_name (str) – The name of the segmentation mask.

• output_table_name (str) – The name of the output table.

• tiling_shapes (Optional[str] (default: None)) – The tiling shapes to use.

• extended_properties (bool (default: False)) – If True, includes extended properties.

• intensity_mode (Literal['mean', 'median'] (default: 'mean')) – The intensity mode to use. Options: “mean”, “median”.

• reference_coordinate_system (str (default: 'global')) – The reference coordinate system to use.

• inplace (bool (default: True)) – If True, modifies the spatialdata object in place. If False, returns the measurements as a tuple of DataFrames.

• scale (default: 'scale0') – The scale to measure.

Return type:

SpatialData | tuple[DataFrame, DataFrame]

Returns:

If inplace is True, returns the modified spatialdata object. If False, returns a tuple of DataFrames containing the measurements.