I’ve just started playing around with CellProfiler as it looks like a great piece of software,
I would like to explore it as an alternative to Acapella which came with our Opera microscope, however I am having some trouble understanding how to deal with my images.
What I normally do is load a flex file that will contain GFP and RFP channels and 5 stacks in each, I have managed to load the flex files using the latest trunk build of cellprofiler but how do i deal with z-stacks? it seems to load as a single image.
I only want to identify objects in the mid-section of the cells, but i would normally measure variance in pixel intensity across all images and choose the image with the lowest variance in intensity as a way to find the midsection in the stack as it can vary well to well in a high-thoughput screen. This image would then be used for cell image analysis.
An example of the image files i use can be found here: http://www.qfpost.com/download.do?get=9e22847379537cfe1dcc5dd4001f1cb2
any help would be much appreciated