After using the protocol set up to convert amnis .cif files to montages easily readable by cellprofiler, I looked at some of the resulting cell images. Using the “View Images” tool in the File menu, it appears that the images have lost resolution during the conversion. Is this the case, or is the image viewer showing lower res images?
Here is a screenshot of what I mean: the images on the left are those viewed in IDEAS, on the right are CellProfiler. Thanks for any advice.