Due to a combination of circumstances, I need to convert from a single-file 32-bit gray-scale virtual stack to a multiple-file 8-bit gray-scale rotated-and-cropped stack. I want to do this using ImageJ’s macro language and already have an idea of how to do this by iterating through the slices with a for loop. However, I was hoping to take advantage of ImageJ’s batch processor instead. Right now, the only thing holding me back from doing this is I cannot figure out how to specify the output folder. The output in Plugins > Macros > Record… is not correct. It gives run(“Virtual Stack…”, “output=/path/to/output/folder output=TIFF text1=[macro]”). From trial and error, I have determined the output is for the output format, not the output folder.
Does anyone know how to specify the output folder?
Actually, I am having trouble getting the macro call for the format-specific open function. So I can’t actually use a macro to to iterate through the different stacks. It would still be good to know for future reference though.