ImageJ Macro for helping the manual labeling of ROIs. This is intended to be used to manually evaluate whether a cell has nuclear mCherry or not.
Each plane will need to be done seperately, so pick a plane to evaluate (e.g. P0), make a substack of the relevant planes (e.g. if your ROIs for P0 span from slice 5-40, you can estimate +/- 20 from the mean).
For the reference stack I usually will put the CellPose image at the top and bottom of the Z-stack so that you can see the functional image 1st, e.g. concatenate it to the start and the end of your structural image.
Operating instructions:
Change the directory to where you want it to save the ref images and the results ParentD="Y:/DRGS project/P0/"; //where to save the files and the results
Have your ROIs loaded into imageJ and your reference structural Z-stack already open.
Run the macro and evaluate. I usually find that the structural and the functional ROIs rarely line up 1:1 due to warping during the K30, so look for the similar shape rather than the exact XY coordinates.
If your cell doesn't show up in the Max Activity projection or during the K30 strucutral stack due to a low S:N such as in the example below
Use other cells as landmarks to find the right range of Z-plane, e.g. find the cell that lines with the any ROI at the highest and lowest Z-plane and then search within that range. Even including +/-3 zstacks of Z-drift the red nucleus should be visible so if there is no nucelus assume it's excitatory.
Example of intended useage https://youtu.be/iI1-M3u2FjM
Variaibles you can change if desired, but default is fine
AllROIOverlays=1 //set to 1 to include all ROIs or only the 1 of interest
SizeOfFOV=35 //this is in pixels +/- the center of the ROI
xd=1150; //coordinate of the Dialog in X pixel on screen, adjust as necessary or preferred
yd=1110; //coordinate of the Dialog in Y pixel on screen
Mag=7; //adjust to set the amount of zoom