| Image name |
Source file name, including subdirectory |
| ROI label |
Unique ROI (cell or nucleus) ID; matches the pixel value in the ROI segmentation mask |
| x |
The x-coordinate (pixels) of the ROI within the image |
| y |
The y-coordinate (pixels) of the ROI within the image |
| z |
The z-coordinate (pixels) of the ROI within the image |
| ROI volume pix |
Volume (or area, for 2D images) of the ROI in pixels. |
| ROI volume um |
Volume of the ROI in µm3 (or area in µm2, for 2D images) |
| [Fl] mean intensity per ROI |
Average pixel intensity of the [Fl] channel inside the ROI. Calculated for each fluorescent channel in the image |
| [Fl] integrated intensity per ROI |
The sum of all pixel intensities of the [Fl] channel inside the ROI. Calculated for each fluorescent channel in the image |
| [Fl] mean background intensity |
Average pixel intensity of the [Fl] channel in the background (outsize of ROI); will have the same value for all ROI in the image |
| [Fl] integrated background intensity |
The sum of all pixel intensities of the [Fl] channel in the background (outsize of ROI); will have the same value for all ROI in the image |
| [Fl] entropy |
Entropy of the [Fl] channel inside the ROI |
| Pearson correlation coefficient [Fl] vs [Fl*] |
Pearson correlation coefficient between each pair of fluorescent channels [Fl] and [Fl*] inside the ROI |
| Pearson correlation p value [Fl] vs [Fl*] |
p-value for the Pearson correlation coefficient between each pair of fluorescent channels [Fl] and [Fl*] inside the ROI |
| Mutual information [Fl] vs [Fl*] |
Mutual information between each pair of fluorescent channels [Fl] and [Fl*] inside the ROI |
| number of [P] puncta |
Number of puncta detected in the [P] channel and assigned to the current ROI. This will correspond to the individual puncta measurements (Table above) with matching “Image name” and “cell label” values and “channel”=[P]. Calculated for each channel [P] specified as puncta channel |
| average [P] puncta volume pix per ROI |
Average volume in pixels of puncta detected from channel [P] in the current ROI |
| average [P] puncta volume um per ROI |
Average volume in µm3 (or area in µm2, for 2D images) of puncta detected from channel [P] in the current ROI |
| total [P] puncta volume pix per ROI |
Total volume in pixels of puncta detected from channel [P] in the current ROI |
| total [P] puncta volume um per ROI |
Total volume in µm3 (or area in µm2, for 2D images) of puncta detected from channel [P] in the current ROI |
| average [P] puncta distance to ROI border um per nucleus |
Average distance in µm (in 3D) from the puncta’s centers of mass to the ROI border |
| [Fl] mean intensity inside [P] puncta |
The average intensity of the [Fl] channel inside puncta detected in the [P] channel in the current ROI. For [Fl]=[P], this will correspond to the dense phase concentration |
| [Fl] mean intensity outside [P] puncta |
The average intensity of the [Fl] channel outside puncta detected in the [P] channel in the current ROI. For [Fl]=[P], this will correspond to the light phase concentration |
| [Fl] integrated intensity inside [P] puncta |
The sum of all intensities of the [Fl] channel inside puncta detected in the [P] channel in the current ROI. |
| [FL] integrated intensity outside [P] puncta |
The sum of all intensities of the [Fl] channel outside puncta detected in the [P] channel in the current ROI. |
| Overlap coefficient [P]_[P*]_coloc |
Overlap coefficient (overlap over union) for the current ROI for puncta masks detected from each pair of puncta channels [P] and [P*]. This is a measure of colocalization between puncta detected in different channels |