Call ImarisConvert from ImageJ

Triggered by the discussion in BigStitcher HEADLESS fails, I’d like to share a little tool that allows converting image files to the Imaris format from within ImageJ:

This plugin allows to:

  • configure the location of ImarisConvert.exe via Edit > Options > Imaris Converter…
  • convert any file to the Imaris5 (.ims) format via FMI > Imaris > Convert to Imaris5 format

And of course, batch processing is included for free via the Batch button in the ImageJ search interface.

@CellKai, as I saw you’re calling ImarisConvert.exe from a Python wrapper script here:

… you (and others, of course) might be interested in also using/testing the commands we provide in the ImageJ plugin to call ImarisConvert from within ImageJ.

In my experience, it is easier for many users to run their batch processing from within the ImageJ user interface, instead of having to call a python script from the command line. (Your mileage may vary, of course. :wink: )

For anyone who wants to test it (as long as I don’t serve it via update site…): download faim-imagej-imaris-tools-0.0.1.jar and put it into your


Hi @imagejan,

thanks for this! I just tested it an it works like a charm out of the box :smiley:
the usual awesome :star_struck:

I agree that its easier for users this way!

Dear @imagejan,
Do you know how to modify the color and rename every channel with ImageJ, to directly have the channel set correctly in Imaris.
Every time I tried to use the merge channel function in imageJ + imaris converter, I have a file with channel 1 blue, channel 2 green, channel 3 red and channel 4 to 6 in gray.