I want to analyze specific areas, any method that you recommend?

I am looking for some way to analyze only the areas that contain a square in the image.
Or better yet, if you have a tip to analyze from a specific area.

That is the problem I have.

You draw manually the rectangle right ?
You can use the rectangular ROI selection in imageJ, press t to add it to the RoiManager and then click “measure” to measure mean gray level for instance.

Is that answering your question ?

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Are you looking for a solution in OpenCV (since you tagged it), and python, or ImageJ, or anything will do?

ImageJ has ROIs + Roi manager to efficiently treat subregions. While in python you would probably simply crop your numpy array of the image to the region of interest.

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What I seek is to automate the measurement of a part of the root, which is what is in the rectangle. my idea is that in a blue screen it has a sector (the rectangle) that delimits to solo analyze that sector.