Is there a way to run FIji's Stitching from a script?

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I think the answer is NO, but just in case I’d like to ask this question: is there a way to automate FIji’s Stitching from a script?

As far as I could see, there is no API prepared for Stitching plugin. So I’ll have to use Fiji’s GUI.

Is there a way to automate the GUI control of Fiji?


I guess you’re referring to Fiji’s Plugins > Stitching > Grid/Collection Stitching command, right? I’m running it in batch from IJ1 macro like this:

From other script languages you can usually call (as recorded from the macro recorder e.g. in Javascript mode):"Grid/Collection stitching", "type=[Positions from file] order=[Defined by TileConfiguration] directory=test layout_file=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 compute_overlap computation_parameters=[Save memory (but be slower)] image_output=[Fuse and display]");

but that will open the result as a new image, which you’d have to get via IJ.getImage() then…

If you’d like to have more control, you can call the Java API directly, as illustrated here:

Note that there’s now BigStitcher which offers a mode that’s scriptable via IJ1 macro language as well:


Thank you. This was much more than I was expecting. Very helpful!!!