Batch Processing without opening image




I order to analyze multiple images I have wrote a script (IJ1 Macro Language) that opens a image run simple conversions (for instance “Subtract background…”, “Median…”, “Watershed…”, etc.), then “Analyze Particles…” and save results. I used to start this script and then hide ImageJ bringing some other window on top, so I can do something else while it running, but recently (after Windows update?) it stops working in such a way. Now every other image is opened as top window and I can’t do anything else but looking on sequence of blinking images.

So, I wondering is there a way to do such analysis without actually opening the image window, i.e. can it be done at background?

Thanks in advance,


Hard to guess without your macro.

However you can avoid the image display with the setBatchMode(arg) function in a macro (and speeding it up), see:


You can take a look at KNIME Image Processing if you want to run automated analysis on many pictures, especially if you want to also do more advanced analysis of your measurements afterwards. Our ImageJ integration allows you to run ImageJ2 plugins as well as some ImageJ1 macros (they need to be headless, i.e. not requiring any user input), see this post for a very simple example use case Macro for bulk processing/cropping of images