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Hey you all,
I am a total newby with ImageJ but someone told my that the thing I am looking for could maybe be solved by this programme. I searched in the plugins and over here... However, I couldn't find anything helpful till now. Therefore, I hope that someone has a useful advice for me.
Maybe I should start by explaining my problem and what I hope the programme could do for me.:
So what I do is mass spectrometry imaging of tissues, e.g. a mouse brain.
After analysis I end up with (sometimes) thousands of images. Each image gives the intensity distribution of a specific ion signal (standing for specific molecules) over the area measured. So the area is the same for all images but depending on the ion signal I look at, different features are highlighted in the picture by a high intensity in the color scale.
There are different color scales I can use. To keep it simple, imagine I would just use a grey scale so features highlighted will become white.
Now imagine I am interested in one specific feature and know how this one looks like. But now I want to know which signals highlight this specific feature.
What I basically have to do then (till now) is go through all the images by hand and look for high signal intensity within my region of interest. If the feature of interest is highlighted I take the picture and put it in another folder to collect all images that highlight the same feature. It would be so nice if this could be automated...
I would imagine it like this:
a) Define ROI: First, I search one picture where the interesting feature is highlighted and define a ROI either by hand or by thresholding.
b) I should be able to somehow tell the programme that it has to search all images in one folder (500-1000 other images) and look if there is a significant signal to background relation within the specific ROI.
c) If so, the programme should move the image file to a specific folder.
Would be marvellous if that could somehow work. Maybe someone has an idea or hint?
Thank you a lot
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