Reference channel features description
Description of all the features saved by SpotMAX for each segmented object
(e.g., single cells, see Cells segmentation end name
parameter) based on the reference channel segmentation masks (see the
Segment reference channel parameter).
There are two types of features: a) single segmented object level, called “whole object” (e.g., volume of the segmented reference channel in the single cell), and b) sub-object level, where the reference channel mask in the single object is separated into non-touching objects.
These features can be used to filter the reference channel masks using the
parameter Features for filtering ref. channel objects and they can
be save to a CSV file using the paramter Save reference channel features.
Background metrics - whole object
Mean: column name
background_ref_ch_mean_intensity.Sum: column name
background_ref_ch_sum_intensity.Median: column name
background_ref_ch_median_intensity.Min: column name
background_ref_ch_min_intensity.Max: column name
background_ref_ch_max_intensity.25 percentile: column name
background_ref_ch_q25_intensity.75 percentile: column name
background_ref_ch_q75_intensity.5 percentile: column name
background_ref_ch_q05_intensity.95 percentile: column name
background_ref_ch_q95_intensity.Standard deviation: column name
background_ref_ch_std_intensity.
Intensity metrics - whole object
Mean: column name
ref_ch_mean_intensity.Background corrected mean: column name
ref_ch_backgr_corrected_mean_intensity.Sum: column name
ref_ch_sum_intensity.Background corrected sum: column name
ref_ch_backgr_corrected_sum_intensity.Median: column name
ref_ch_median_intensity.Min: column name
ref_ch_min_intensity.Max: column name
ref_ch_max_intensity.25 percentile: column name
ref_ch_q25_intensity.75 percentile: column name
ref_ch_q75_intensity.5 percentile: column name
ref_ch_q05_intensity.95 percentile: column name
ref_ch_q95_intensity.Standard deviation: column name
ref_ch_std_intensity.
Morphological metrics - whole object
Volume (voxel): column name
ref_ch_vol_vox.Volume (fL): column name
ref_ch_vol_um3.Number of fragments: column name
ref_ch_num_fragments.
Region properties - whole object
These are calculated using the function skimage.measure.regionprops from
the scikit-image library. The following properties are calculated:
Major axis length: column name
ref_ch_major_axis_length.Minor axis length: column name
ref_ch_minor_axis_length.Equivalent diameter: column name
ref_ch_equivalent_diameter.Volume (voxel): column name
ref_ch_area.Solidity: column name
ref_ch_solidity.Extent: column name
ref_ch_extent.Volume of the filled region: column name
ref_ch_filled_area.Volume of the bounding box: column name
ref_ch_bbox_area.Area of the convex hull image: column name
ref_ch_convex_area.Euler number: column name
ref_ch_euler_number.Maximum Feret’s diameter: column name
ref_ch_feret_diameter_max.Orientation (angle): column name
ref_ch_orientation.Perimeter: column name
ref_ch_perimeter.Perimeter (Crofton): column name
ref_ch_perimeter_crofton.Perimeter (Crofton): column name
ref_ch_perimeter_crofton.Circularity: column name
ref_ch_circularity. Circularity is calculated as follows:\[\mathrm{circularity} = \frac{4\pi A}{P^2}\]where \(A\) is the area of the object and \(P\) is the perimeter of the object.
Roundness: column name
ref_ch_roundness. Roundness is calculated as follows:\[\mathrm{roundness} = \frac{4A}{\pi M^2}\]where \(A\) is the area of the object and \(M\) is the major axis length of the object.
Intensity metrics - sub-object
Mean: column name
sub_obj_ref_ch_mean_intensity.Background corrected mean: column name
sub_obj_ref_ch_backgr_corrected_mean_intensity.Sum: column name
sub_obj_ref_ch_sum_intensity.Background corrected sum: column name
sub_obj_ref_ch_backgr_corrected_sum_intensity.Median: column name
sub_obj_ref_ch_median_intensity.Min: column name
sub_obj_ref_ch_min_intensity.Max: column name
sub_obj_ref_ch_max_intensity.25 percentile: column name
sub_obj_ref_ch_q25_intensity.75 percentile: column name
sub_obj_ref_ch_q75_intensity.5 percentile: column name
sub_obj_ref_ch_q05_intensity.95 percentile: column name
sub_obj_ref_ch_q95_intensity.Standard deviation: column name
sub_obj_ref_ch_std_intensity.
Morphological metrics - sub-object
Volume (voxel): column name
sub_obj_vol_vox.Volume (fL): column name
sub_obj_vol_fl.
Region properties - sub-object
These are calculated using the function skimage.measure.regionprops from
the scikit-image library. The following properties are calculated:
Major axis length: column name
sub_obj_ref_ch_major_axis_length.Minor axis length: column name
sub_obj_ref_ch_minor_axis_length.Equivalent diameter: column name
sub_obj_ref_ch_equivalent_diameter.Solidity: column name
sub_obj_ref_ch_solidity.Extent: column name
sub_obj_ref_ch_extent.Volume of the filled region: column name
sub_obj_ref_ch_filled_area.Volume of the bounding box: column name
sub_obj_ref_ch_bbox_area.Area of the convex hull image: column name
sub_obj_ref_ch_convex_area.Euler number: column name
sub_obj_ref_ch_euler_number.Maximum Feret’s diameter: column name
sub_obj_ref_ch_feret_diameter_max.Orientation (angle): column name
sub_obj_ref_ch_orientation.Perimeter: column name
sub_obj_ref_ch_perimeter.Perimeter (Crofton): column name
sub_obj_ref_ch_perimeter_crofton.Circularity: column name
sub_obj_ref_ch_circularity.Circularity is calculated as follows:
\[\mathrm{circularity} = \frac{4\pi A}{P^2}\]where \(A\) is the area of the object and \(P\) is the perimeter of the object.
Roundness: column name
sub_obj_ref_ch_roundness.Roundness is calculated as follows:
\[\mathrm{roundness} = \frac{4A}{\pi M^2}\]where \(A\) is the area of the object and \(M\) is the major axis length of the object.