Manually combining ROIs using overlay

Hi all,

relative newcomer to FIJI/imageJ, I am trying to work out how to do manual curation of ROIs automatically generated using thresholding & particle analyser. The data is neural imaging, so is composed of fluorescent cell bodies (easy to segment) and axon processes - this is where the problem arises

Basically, the axons often appear as multiple points along a line (where the axon goes into and out of the z-plane focus), so the thresholding picks them up as such. The resulting ROI map will then have multiple ROIs lined up along the axons path - in order to properly analyse I will need to combine these individual ROIs into non-overlapping multiple selections.

What I am envisioning is being able to draw a line using the line tool, which intersects the ROIs I can see are points along an individual axon, then combine these into an ROI.

If anyone knows how I could get this working, that would be awesome,


You can combine multiple ROIs in the ROI Manager using this macro:

//this script combines the first two ROIs in the ROI Manager
roiManager("select", 0);
roiManager("select", 1);

Maybe this helps you finding à solution.