Aggregated features description
Description of all the features saved by SpotMAX for each segmented object
(e.g., single cells, see Cells segmentation end name
parameter) and the corresponding column name. These are simple aggregations
like averaging and sum.
See also
For more details, see the corresponding feature in the Single-spot features description
section. For example, the aggregated metric with column name
mean_sigma_x_fit is the mean of the single spot metric called
sigma_x_fit between spots of the same input object (e.g., single cells).
Spot detection
Number of spots: column name
num_spots.Number of spots inside ref. ch.: column name
num_spots_inside_ref_ch.
Spotfit size metric
Mean radius x- direction: column name
mean_sigma_x_fit.Mean radius y- direction: column name
mean_sigma_y_fit.Mean radius z- direction: column name
mean_sigma_z_fit.Std. dev. radius x- direction: column name
std_sigma_z_fit.Std. dev. radius y- direction: column name
std_sigma_y_fit.Std. dev. radius z- direction: column name
std_sigma_x_fit.
Spotfit intens. metric
Sum of total integral gauss. peak: column name
sum_tot_integral_fit.Sum of foregr. integral gauss. peak: column name
sum_foregr_integral_fit.Sum of amplitude gauss. peak: column name
sum_A_fit_fit.Mean backgr. level gauss. peak: column name
mean_B_fit_fit.
Spotfit Goodness-of-fit
Mean RMS error gauss. fit: column name
mean_RMSE_fit.Mean normalised RMS error gauss. fit: column name
mean_NRMSE_fit.Mean F-norm. RMS error gauss. fit: column name
mean_F_NRMSE_fit.
Segmented objects size (e.g., single cells)
Area of the segmented object (pixel): column name
cell_area_pxl.Area of the segmented object (micro-m^2): column name
cell_area_um2.Estimated 3D volume from 2D mask (pixel): column name
cell_vol_vox. To calculate cell volume from a 2D mask, the mask is first aligned along its major axis. Next, it is divided into slices perpendicular to the major axis, each slice with width equal to 1 pixel. Assuming rotational symmetry of each slice around its middle axis parallel to the mask’s major axis, SpotMAX computes the volume of the resulting cylinder. Finally, the volumes of each cylinder are summed to obtain the total volume.Estimated 3D volume from 2D mask (fl): column name
cell_vol_fl. Estimated 3D volume from 2D mask in pixels converted to femtoliters (equivalent to \(\mu m^3\)) using the pixel size provided in the parameters.3D volume from 3D mask (voxel): column name
cell_vol_vox_3D.3D volume from 3D mask (fl): column name
cell_vol_fl_3D.