how do i extract out each pixel value in that region

so basically I have matrix and I have convert it into a grey image. How can make a region on all cells and extract out all of the each individual region pixel setting it to a variable.

Answer 1

[Image Analyst]

It depends. If you have good control over your exposure, you can use a fixed threshold and then use regionprops. See my Image segmentation Tutorial for a demo. http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862. If the exposure varies image by image then you'll have to take that into account. If you need to take into account the absence of color in a spot (so that it looks just like the background), then you'll have to use a template - either a predefined one or one determined by what blobs are there in the image (which is not robust if you have most of the spots missing).