Running ImageJ within MATLAB



I edited the section Running ImageJ within MATLAB and here some thoughts and questions.

  1. The method IJM.importDataset mentioned in the original does not exist for ImageJ-MATLAB 0.7.2. Also the example just below uses IJM.getDatasetAs instead. So, to make sense of it, I replaced IJM.importDataset with IJM.getDatasetAs.
  2. How can I add a screenshot to this page? I wanted to add a screenshot of ImageJ to give an idea of what happens. ------ SOLVED
  3. The paragraph “Additionally, the Scripting-MATLAB library also includes …” is unclear. I don’t quite understand what Scripting-MATLAB actually does. This paragraph mention IJM, which is short of net.imagej.matlab.ImageJMATLABCommands class, but it appears that it’s part of imagej-matlab rather than Scripting-MATLAB. (See Is IJM (net.imagej.matlab.ImageJMATLABCommands) dependent on Scripting-MATLAB???

Cannot run ImageJ.m from MATLAB with Java 1.8

As to Q2, Once you’re logged in, at the bottom of a web page, you’ll see TOOLS > Upload File and you add images from there.


After logging in to the wiki (using https:// is recommended), you will see an Upload file link at the bottom of each page. Upload an image, and then reference it in the wiki markup like [[File:myimage.png|300px]]. See Help:Images for details.

For the ImageJ-MATLAB-related questions (1) and (3), I invited @hinerm, the maintainer of that project, to respond here. If you don’t hear back within a few days, feel free to ping again here and I’ll try to find time to dig in and investigate and respond.


Since I posted this thread, I’ve added quite a lot of stuff to, especially Prerequisites and Running ImageJ within MATLAB sections, in the hope that this will help other people.

My general impression is that the number of people who use MATLAB with open source image analysis tools like ImageJ and OMERO is limited. Both in ImageJ and OMERO, they say tools for MATLAB are there, but you essentially have to understand and use Java API within MATLAB.

Still, building the workflow in pure Java is a pain to me. Because I use MATLAB for signal processing in general, it makes sense to me to use the same platform for image processing.