Automating substraction, Weka, and intensity measurement

Hello there,
I’m new to both ImageJ/Fiji and , so my question may be kind of basic.

I want to use Fiji to automatically mark cells on my image.
I took both pictures of DAPI, to mark the nucleus, and the fluorescent protein (GFP).
Now I want to use Fiji to automatically find these cells and nuclei. Then I want to “delete” the nucleus from the fluorescent picture. After that I want to measure the intensitiy of the cells without the nucleus.
I also want to measure the intensity of the nucleus alone, so I have to cut only the cytoplasm and leave only the nucleus of the fluorescent picture.

Basically I want to know how much of my protein is in the cytoplasm compared to the nucleus.

I quickly found Weka trainable segmentation to mark my cells. I also discovered that you can just substract images from one another.

Now I can substract the images to have one with only the cytoplasm and one with only the nucleus. Of both I now can mark the cell/nucelus and measure the intensity.

I now want to use a macro to automate the substraction, the marking by Weka, and the measuring of the intensity.

I have like zero experience in programming, so if anybody had a macro I could copy that would be great. A macro that can do some of the parts would equally be awesome.

Thank you very much in advance,


P.S.: sorry for the long text, but I really want you guys to understand what my problem is and with my lack of knowledge in that matter I could not shorten my question…


For starting out scripting in ImageJ/Fiji - here are some super helpful links:

Start with the workshop video/slides… there are examples of code in there that you can use to start working with. Also - just searching here on the forum - you might find some helpful macro code that you can adapt.