Features

The following table gives an overview of all available features with an explanation and an example output (depending on your image an parameter configuration the number of features you get might vary). The features can be structured in several categories:

Category	Configuration	Explanation
single cell features	always	The general features extracted from the image.
nucleus features*	nucleus channel given	All features belonging to the nucleus of the cell.
organelle features*	organelle channel given	All features belonging to the organelle of a cell.
junction features*	junction channel given	All features belonging to the junctions of a cell
marker features* marker membrane features marker nucleus features marker cytosol features	expression marker channel given	All features belonging to the expression marker. If a nucleus channel is given, marker nucleus features and marker cytosol features are automatically appended.
neighborhood features	always	Statistical properties of a feature of interest (FOI) specified. Includes neighborhood statistics. Feature of Interest (FOI) must be specified. Default is “area”.
group features	always	Group properties. Image wise. Includes Morans I correlation analysis. Feature of interest (FOI) must be specified.

Note

Features highlighted with a * are optional.

Single cell features

Feature	Explanation
filename	The filename where the cell was found.
img_hash	The sha1 hexadecimal hash of the image content.
label	The cellpose segmentation label of the particular cell.
cell_X	The X coordinate (horizontal axis) of the center of the cell.
cell_Y	The Y coordinate (vertical axis) of the center of the cell.
cell_shape_orientation_deg	Long axis of ellipsoid fit of the cell in degree.
cell_shape_orientation_rad	Long axis of ellipsoid fit of the cell in rad.
cell_major_axis_length	Length of the major axis of the cell.
cell_minor_axis_length	Length of the minor axis of the cell.
cell_eccentricity	Value for the elongation of the cell. Between 0 and 1, where 0 correspond to a perfect circular cell and 1 for a strongly elongated cell.
cell_major_to_minor_ratio	Ratio between the major and the minor axis of the cell.
cell_area	The area of the cell.
cell_perimeter	The perimeter of the cell.
cell_circularity	Cell shape circularity computed from 4*pi*(area/perimeter^2), also see https://imagej.nih.gov/ij/plugins/circularity.html .
cell_shape_index	Cell shape index computed from cell_perimeter / np.sqrt(cell_area), see for example https://doi.org/10.1038/nphys3471

Nucleus features

Feature	Explanation
nuc_X	X position (horizontal axis) of the cell nucleus.
nuc_Y	Y position (vertical axis) of the cell nucleus.
nuc_displacement_orientation_rad	The displacement orientation of the nucleus from the center of the cell in rad.
nuc_displacement_orientation_deg	The displacement orientation of the nucleus from the center of the cell in deg.
nuc_shape_orientation_rad	Long axis of ellipsoid fit of the nucleus in rad.
nuc_shape_orientation_deg	Long axis of ellipsoid fit of the nucleus in deg.
nuc_major_axis_length	The length of the major axis of the nucleus.
nuc_minor_axis_length	The length of the minor axis of the nucleus.
nuc_area	The area of the nucleus.
nuc_perimeter	The perimeter of the nucleus.
nuc_eccentricity	Value for the elongation of the nucleus. Between 0 and 1, where 0 correspond to a perfect circular nucleus and 1 for a strongly elongated nucleus.
nuc_major_to_minor_ratio	Ratio between the major and the minor axis of the nucleus.
nuc_circularity	Nucleus shape circularity computed from 4*pi*(area/perimeter^2), also see https://imagej.nih.gov/ij/plugins/circularity.html .
nuc_shape_index	Nucleus shape index computed from cell_perimeter / np.sqrt(cell_area).

Organelle features

Feature	Explanation
organelle_X	The X coordinate (horizontal axis) of the center of the cell organelle.
organelle_Y	The Y coordinate (vertical axis) of the center of the cell organelle.
nuc_organelle_distance	Distance from cell organelle to the nucleus.
organelle_orientation_rad	The orientation in rad of the organelle to the nucleus
organelle_orientation_deg	The orientation in deg of the organelle to the nucleus

Marker features

Feature	Explanation
marker_mean_expression	Mean expression of the channel with the marker.
marker_sum_expression	The absolute sum of the expression of the marker.
marker_centroid_X	The X coordinate (horizontal axis) of the center of the marker expression.
marker_centroid_Y	The Y coordinate (vertical axis) of the center of the marker expression.
marker_centroid_orientation_rad	Intrinsic asymmetry of the cell.
marker_centroid_orientation_deg	Intrinsic asymmetry of the cell.
marker_mean_expression_mem	Mean membrane expression.
marker_sum_expression_mem	The absolut sum of the membrane expression.
marker_mean_expression_nuc	The mean expression of the nucleus.
marker_sum_expression_nuc	The absolut sum of the nucleus expression.
marker_mean_expression_cyt	The mean expression of the cell cytosol.
marker_sum_expression_cyt	The absolut sum of the cell cytosol expression.
marker_nucleus_orientation_rad	The orientation in rad of the marker centroid to the nucleus.
marker_nucleus_orientation_deg	The orientation in rad of the marker centroid to the nucleus.
marker_cue_intensity_ratio	The ratio of the left vs right cell membrane intensity in cue direction.
marker_axial_cue_intensity_ratio	The ratio of the sum of cell membrane quarters in cue direction and the total membrane intensity.

Junction features

Feature	Explanation
junction_centroid_X	The X coordinate (horizontal axis) of the center of the junction expression.
junction_centroid_Y	The Y coordinate (vertical axis) of the center of the junction expression.
junction_perimeter	The perimeter of the junction area.
junction_protein_area	The area with junction protein expression.
junction_mean_intensity	The mean junction intensity value.
junction_protein_intensity	The mean protein intensity by area.
junction_interface_linearity_index	The linearity index of the junction.
junction_interface_occupancy	The ratio between junction area and junction protein area.
junction_intensity_per_interface_area	The ratio between the junction protein intensity and the junction area.
junction_cluster_density	The ratio between the junction protein intensity and the junction protein area
junction_centroid_orientation_rad	The orientation in rad of the junction intensity area centroid to the center of the cell.
junction_centroid_orientation_deg	The orientation in deg of the junction intensity area centroid to the center of the cell.
junction_cue_intensity_ratio	The ratio of the left vs right cell membrane intensity in cue direction.
junction_axial_cue_intensity_ratio	The ratio of the sum of cell membrane quarters in cue direction and the total membrane intensity.

Neighborhood features

Feature	Explanation
neighbors_cell	The absolut number of neighbors of the cell.
neighbors_mean_dif_1st	Mean difference of the feature of interest to all first neighbors.
neighbors_median_dif_1st	Median difference of the feature of interest to all first neighbors.
neighbors_stddev_dif_1st	Standard derivation of the difference of the feature of interest to all first neighbors.
neighbors_range_dif_1st	Maximal range of difference of the feature of interest to all first neighbors.
neighbors_mean_dif_2nd	Mean difference of the feature of interest to all second neighbors.
neighbors_median_dif_2nd	Median difference of the feature of interest to all second neighbors.
neighbors_stddev_dif_2nd	Standard derivation of the difference of the feature of interest to all second neighbors.
neighbors_range_dif_2nd	Maximal range of difference of the feature of interest to all second neighbors.

Group features

Feature	Explanation
morans_i	Statistical correlation analysis
morans_p_norm	P-norm of the correlation analysis.