Signal quantification

timagetk.algorithms.signal_quantification.quantify_cell_interface_signal_intensity(signal_img, tissue, cell_ids=None, interface_distance=1.0)[source]

Quantify average image intensity at interfaces between 3D segmented_cells.

Parameters:

  • signal_img (timagetk.SpatialImage or timagetk.MultiChannelImage) – Intensity image with the signal to quantify.

  • tissue (timagetk.components.tissue_image.TissueImage3D) – Labelled image to use for signal quantification.

  • cell_ids (int or list of int, optional) – If None (default), returns values for all cell ids found in tissue. Else, should be a cell id of a list of cell ids. Note that given cell ids are checked for existence within the array.

  • interface_distance (float, optional) – Distance up to which voxels are considered to belong to the interface.

Returns:

dict – Cell interface signal intensity dictionary, {(c1, c2): signal((c1, c2))}` or ``{channel: {(c1, c2): signal((c1, c2))} } if multichannel.

timagetk.algorithms.signal_quantification.quantify_cell_signal_intensity(signal_img, tissue, cell_ids=None, erosion_radius=0.0)[source]

Quantify average image intensity inside 3D segmented_cells.

Parameters:

  • signal_img (timagetk.SpatialImage or timagetk.MultiChannelImage) – Intensity image with the signal to quantify.

  • tissue (timagetk.components.tissue_image.TissueImage3D) – Labelled image to use for signal quantification.

  • cell_ids (int or list of int, optional) – If None (default), returns values for all cell ids found in tissue. Else, should be a cell id of a list of cell ids. Note that given cell ids are checked for existence within the array.

  • erosion_radius (float, optional) – Radius by which to erode cells before averaging signal.

Returns:

dict – Cell signal intensity dictionary, {cid: signal(cid)} for cid in cell_ids or {channel: {cid: signal(cid)} } for cid in cell_ids if multichannel.

timagetk.algorithms.signal_quantification.quantify_nuclei_signal_intensity(signal_img, nuclei_points, nuclei_sigma=0.5)[source]

Quantify image intensity at the level of 3D nuclei points.

Parameters:

  • signal_img (timagetk.SpatialImage) – Intensity image with the nuclei signal to quantify.

  • nuclei_points (numpy.ndarray) – Nuclei 3D positions, in physical XYZ coordinates.

  • nuclei_sigma (float, optional) – Standard deviation of the Gaussian kernel used to average local signal.

Returns:

numpy.ndarray – Nuclei quantified signal values.