I’m running MicaToolbox in the latest version of Fiji (ImageJ 1.52p with Java 1.8.0_202) on Mac OS High Sierra (10.13.6). Should all the Mica Toolbox functions work with this installation, or would you recommend that I use an older version of ImageJ? I was following the ImageJ installation recommendations here:
Most of the MicaToolbox functions seem to run ok. I loaded an image of an X-Rite Mini ColorChecker as a Linear Normalized Reflectance Stack to measure the colour chart and obtained good R^2 correlation values (>0.99). When I use measurements of my colour chart to generate a Cone Mapping Model for my camera and human visual system (CIE 1931) using the command “Generate Cone Mapping Model from Chart”, it produces a file in the Cone Models folder with the extension .java. However, I get a warning from Fiji (ImageJ) that says “The ‘Compile and Run Command’ is not currently supported. We recommend using the Script Editor or an IDE such as Eclipse for plugin development.” Can you suggest a workaround for the warning that ‘Compile and Run’ isn’t supported in Fiji (ImageJ)?
After this warning, not all of the MicaToolbox menus are visible in the Plugins menu, and I have to restart Fiji to get all the menus to appear again. When I try to convert the mspec image to a Cone Catch Image, the newly created Cone Mapping Model for my camera doesn’t appear in the drop-down menu as an option. I realized this is because my Cone Mapping Model with .java extension hasn’t been compiled to run in Fiji (ImageJ), and there isn’t a corresponding .class file in the Cone Models folder.
Hi, the issue is that you’re using FIJI instead of ImageJ. Just follow the installation instructions here. There are various toolbox functions which don’t work in FIJI (which is a just a different fork of ImageJ). The standard NIH ImageJ is well maintained and much less bulky than FIJI (which has lots of cool extra functions, but most of them aren’t useful for animal vision image analysis).
If you do need functions in FIJI rather than ImageJ you could compile the script in ImageJ, then copy the .CLASS file across to your FIJI installation.