Thresholding ‐ Mask

The thresholding/mask tab displays the total intensity (total = sum over the angles) image of the stack to be analyzed with a threshold specified in ILow. The selected dark value has been removed from the intensity (see Dark value for more information on the dark).

Information on the Navigation toolbar can be found here.

The value of ILow can be modified with the ILow slider. The entry box displays the selected ILow which can also be entered manually. The value of ILow used for the analysis is saved in the MS Excel file (see Save output in Options tab).

• For improved visualization, the contrast can be adjusted with the slider on the right hand side of the tab. The selected contrast does not affect the analysis.

  The component of the image below the intensity threshold can be visualized in transparency using the Transparency slider. The selected transparency does not affect the analysis.

• click this button to change the colormaps used in the thresholded image ('hot' or 'gray').
• For improved visualization, a dark or light mode can be selected for the background.
• exports the binary mask in a `.png` format. Three options to create the masks: using selected ROIs only, using the image above threshold, or a combination of both (component of the image above threshold and inside selected ROIs). The file name of the exported mask includes the suffix `_mask` to avoid overwriting an existing mask for the same file. To use it for further analysis, remove this suffix.
• opens the ROI Manager (click here for more details)
• Click this button to open a window for the options to detect edges; Click 'Compute' to determine the edges of the thresholded image as displayed in the Thresholding/Mask tab. Alternatively, contours can be determined from a mask; click 'Download', and select this mask to determine its edges. For more details, see Edge detection. Click 'Cancel' to close the window and inactivate edge detection.