runImageJ cannot find ImageJ plugin

I installed CP 2.2.0 with Conda ( to use runImageJ module, because I need to stick to IHC profiler plugin.

I did specify the plugin directory in the preference, but in runImageJ - command - plugin, I cannot find IHC profiler plugin. what am I missing here?


Can you try: first make a ImageJ script that run your IHC plugin. Build and test your script directly in ImageJ environment. Make sure in this script, you specify your plugin location (/absolute/path/to/IHC/plugin)

Then inside CellProfiler, runImageJ - command - plugin - Run Script…

Hope that helps.

I couldn’t find how to specify the absolute path of a plugin using “run” method, so i took an indirect path like“Compile and Run…”, “compile=/plugin”)

instead of“plugin”)

anyway either works well in ImageJ environment, but when I try runImageJ - command - plugin - Run Script,

it first of all says that the input image has to be Graycolor, which is quite weird.
despite the fact that my input images have to be color, I tried changing the Cellprofiler input image type into Graycolor to see what happens, then runImageJ says “no input image”.

I guess you’re quite near there.

Let’s try to keep the input image as “color”. Then make an extra module downstream “ColorToGray” where you split the red, green, blue channel. Then feed each of them channel to your runImageJ module.

Let’s see if it helps…

do you know which variables exactly runImageJ expects as input and output image names?? i’m customizing the imageJ plugin, so maybe I can make it smoothly connect to runImageJ module if i know some details… i think the ‘no input image’ error has something to do with the naming thing!

RunImageJ doesn’t work in 2.2 or later versions of CP; you’d need to roll back to 2.1.1. Sorry!

May I ask if RunImageJ is fixed in the 2.30 Beta? If not, are there plans to bring it back?

Great job on an excellent program!!

It does not work in any versions after 2.1.1 and is being removed as of 3.0; a replacement is in the works but is not finished yet. Sorry!