Hi Beth and Min,
Thanks for your pointers and help so far.
I wrote the pipeline you suggested, but I have an odd problem.
I get a run error in RescaleIntensity (‘Invalid dimensions for image data’), and I can not open by doubleclicking on the file names for the images from the Images tab. However, when I check ‘No’ for process images as 3D, the modules will run and I can open the images, but I do not get the 9-pane montage that you show in the tutorial.
I can organize the images in Metadata and Groups, but am using 2 of 5 channels