Different ROIs for each slice in video to measure mean grey value

Dear people!

I have multiphoton timeseries of 80 pictures. I want to segment intravascular and extravascular, which I sucessfully did using the threshold function to make a mask and then create a ROI out of that selection, make the inverse and voilà you have the extravascular section (only did cost me two days to figure out haha). However, there is movement in Z within the time series, this is not very uncommon since we inject quite a large volume of dextran. The problem is that using Imaris, I cannot sufficiently correct for that movement. Using a single intravascular and extravascular ROI for the whole video leads to messy mean grey values because sometimes the intravascular signal moves into the extravascular ROI and vica versa. Solution? Make a intra- and extravascular ROI for each picture and measure the MGV for each picture. I was hoping someone has dealt with this before and knows a better way of doing it than first making the ROIs for each picture, than doing the measurement for all the individual ROIs or could maybe help me to automate it a little bit. I am very open to learn!

Since I am under time pressure I will start with the tedious work right now, since I wasn’t able to find any information as to make this process more efficient so far and I am under quite some time pressure.

I already appreciate your help a lot! I can’t seem to be able to add the Tiff, maybe in the comments after I posted it then :slight_smile:

I get an error trying to upload the tiff, I am really sorry!