I use cellprofiler a lot but for 2D images. I am trying to develop these pipelines for the 3D images in our lab. I have a question for the output. For example, one image is quite large, 80 stacks. The output has 12 columns of data per image, so my question is how is it broken down? Can I take an average of these columns and denote this as the mean result of the whole stack?
Also, curious to know if there are any developments for the identify primary objects and other modules will become available for 3D.