Thank you so much for your response!
Hmm. I think this is what I have. I’ve used segmentation editor to outline (using the selection brush tool) a structure across multiple slices, interpolated across these slices, and then added that selection to a designated label. I do this twice for each side of the brain and so I have two separate labels to import into 3D ROI Manager. Then I open the ROI Manager and select “add image”. If all goes well, two labels appear and the log says “adding image:min-max 1 2”. Unfortunately, it seems to be hit or miss. When it doesn’t work the log says “adding image: min-max 31-65535” and no labels appear in the ROI Manager. I should be okay with memory since the files are around 50MB.
I just noticed you were an author of the plug-in. Am I using it correctly? Will “quantif 3D” actually quantify fluorescence within each labeled selection or should I be doing something else? I tried using the 3D object counter but I couldn’t find a threshold level that was limited to the brain region I would like to quantify, which is why I decided to trace it in segmentation editor.
Thank you in advance for your time and advice! I really appreciate your insight.