I’m new to both ImageJ/Fiji and image.sc , 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…