If you drag the folder with the files on ImageJ or (use the import image sequence action by selecting one file - momentarily I use Windows) a dialog pops up to import the sequence as a stack or virtual stack.
I have to enable the option “Sort names numerically” and then the sorting is:
“Sort Names Numerically” When checked, the stack will be opened in numeric file name order (e.g., ‘name1.tif’, ‘name2.tif’, ‘name10.tif’) instead of alphanumeric order (e.g., ‘name1.tif’, ‘name10.tif’, ‘name2.tif’)…
I renamed some example files and it worked for me numerically - to use the terms of the documentation.
Now I can simply iterate over the stack and can make my measurements.
So you can select stack image 1, make your measurements and then save the image
individually with a new name.
If you need human interaction after saving the image even that is possible with a stack (after
setSlice() - see example).
And more examples here:
For a wait dialog, see: