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Hi all,
I’ve been working with ImageJ for analysis of immunihistochemically stained sections of muscle tissue, in which cells (muscle fibres) are visible by their membranes. Until now, I’ve been using the membranes (by thresholding that channel and then skeletonizing the lines that they form) to define the borders of the cells, and in any further steps I’ve been analyzing the cells themselves.
This is fairly easy to do by using the Analyze Particles function: the software recognizes the cells.
However, now I also want to analyze staining within the membrane, and therefore, I want to select the area of the membranes themselves, without the cells, and then perform measurements within this selection.
So I thresholded the membrane channel and made a binary image of it. I can select the membranes, but when I do, it selects everything within that area. So also the cells (which are packed together, the membranes form an interconnected set of lines on the image). I can deselect the cells by hand, using the Alt key, but on some of the images, there’s 300 cells or so, so I thought perhaps this can be automated.
Does anyone know of, or can anyone think of, a way to do this? Search for these ‘holes’ within a current selection and exclude them?
Thanks in advance,
Rachel
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