Features

Polarity-JaM provides a wide range of features that can be extracted from your images. Depending on the input image and the configuration of the feature extraction, different features are calculated. Thereby the features can be categorized from two different viewpoints:

The target of the feature extraction (e.g. single cell, nucleus, organelle, junction, marker, marker nucleus, marker cytosol, cell neighborhood)
The category of the feature (e.g. identification, localization, polarity, morphology, topology)

Lets first look at the feature types before we dive into the individual features for each target.

Feature types

The table below provides an overview of all available features, along with explanations and example outputs. Depending on your image and parameter configuration, the number of features may vary. Polarity-JaM extracts features based on the configured target, ensuring that all available feature categories are always extracted. These features can be organized into several categories:

Type: Identification & Localization

Localization and identification features are used to identify and locate the object of interest in the image. These features are essential for the subsequent analysis of the image data.

Type: Morphology

Morphological features characterize the shape and size of the object of interest. These can be further classified into geometric features, which describe the object’s overall shape; structural features, which detail the internal structure; and ratio-based features, which involve calculations of various proportions.

Type: Polarity

Polarity features characterize the orientation and asymmetry of the object of interest. Broadly, these can be divided into directional features, which describe the orientation of two objects relative to one another, and axial features, which define the orientation of an object relative to a reference axis. Additionally, predefined axial asymmetry features quantify an object’s asymmetry or the asymmetry of its intensity relative to a reference axis by calculating proportions.

It is not straightforward to understand the difference of axial and directed polarity. Directed polarity can have values between 0 and 360 degrees, while axial polarity is a value between 0 and 180 degrees.

See the following two illustrations to understand the difference:

axial polarity (left) and directed polarity (right)

Type: Intensity

Intensity features characterize the object’s intensity and expression levels. The intensity within different regions can be summed, averaged, or compared using ratios or proportions.

Type: Topology

Topology features describe the spatial relationships between objects in an image. These features are useful for analyzing the distribution of objects and their interactions within the image. Specifically, we focus on the connectivity (neighborhood) and spatial arrangement properties of the objects.

Targets

We offer features for extracting various targets and their combinations. The image below illustrates the different targets.

The following demonstrates how to extract features from a multichannel image for different targets and the required configuration.

Target	Required configuration	Description
single cell	segmentation	The general features extracted from the image.
nucleus	segmentation + nucleus channel	All features belonging to the nucleus of the cell.
organelle	segmentation + organelle + nucleus channel	All features belonging to the organelle of a cell.
junction	segmentation + junction channel	All features belonging to the junctions of a cell
marker	segmentation + expression marker channel	All features belonging to the expression marker
marker nucleus	segmentation + expression marker + nucleus channel	All features belonging to the expression marker and nucleus
marker cytosol	segmentation + expression marker + nucleus channel	All features belonging to the expression marker and cell without nucleus
cell neighborhood	segmentation + FOI	Statistical properties of a feature of interest (FOI). Includes neighborhood statistics. Default FOI is “area”.
group	segmentation + FOI	Group properties. Image wise. Includes Morans I correlation analysis of the feature of interest (FOI). Default FOI is “area”

Note

When a segmentation is not provided during input it will be calculated.

Target: Single cell

Feature Name	Category	Description
filename	None	The filename where the cell was found.
img_hash	None	The sha1 hexadecimal hash of the image content.
label	identification	The cellpose segmentation label of the particular cell.
cell_X	localization	The X coordinate (horizontal axis) of the center of the cell.
cell_Y	localization	The Y coordinate (vertical axis) of the center of the cell.
cell_shape_orientation_deg	polarity	Long axis of ellipsoid fit of the cell in degree.
cell_shape_orientation_rad	polarity	Long axis of ellipsoid fit of the cell in rad.
cell_major_axis_length	morphology	Length of the major axis of the cell.
cell_minor_axis_length	morphology	Length of the minor axis of the cell.
cell_eccentricity	morphology	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 cel
cell_major_to_minor_ratio	morphology	Ratio between the major and the minor axis of the cell.
cell_area	morphology	The area of the cell.
cell_perimeter	morphology	The perimeter of the cell.
cell_circularity	morphology	Cell shape circularity computed from 4pi(area/perimeter^2), also see https://imagej.net/ij/plugins/circularity.html .
cell_shape_index	morphology	Cell shape index computed from cell_perimeter / np.sqrt(cell_area), see for example https://doi.org/10.1038/nphys3471 .

Target: Nucleus

Feature	Category	Description
nuc_X	localization	X position (horizontal axis) of the cell nucleus.
nuc_Y	localization	Y position (vertical axis) of the cell nucleus.
nuc_displacement_orientation_rad	polarity	The displacement orientation of the nucleus from the center of the cell in rad.
nuc_displacement_orientation_deg	polarity	The displacement orientation of the nucleus from the center of the cell in deg.
nuc_shape_orientation_rad	polarity	Long axis of ellipsoid fit of the nucleus in rad.
nuc_shape_orientation_deg	polarity	Long axis of ellipsoid fit of the nucleus in deg.
nuc_major_axis_length	morphology	The length of the major axis of the nucleus.
nuc_minor_axis_length	morphology	The length of the minor axis of the nucleus.
nuc_area	morphology	The area of the nucleus.
nuc_perimeter	morphology	The perimeter of the nucleus.
nuc_eccentricity	morphology	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	morphology	Ratio between the major and the minor axis of the nucleus.
nuc_circularity	morphology	Nucleus shape circularity computed from 4pi(area/perimeter^2), also see https://imagej.net/ij/plugins/circularity.html .
nuc_shape_index	morphology	Nucleus shape index computed from cell_perimeter / np.sqrt(cell_area).

Target: Organelle

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

Note

Here Golgi has been exemplary chosen as a organelle. The features are generic and can be applied to any organelle.

Target: Marker

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

Target: Junction

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

Target: Topology - neighborhood

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