I’m running into a bit of trouble trying to perform illumination correction with images of mammalian cells under higher magnification (60X). The images were generated using an ImageXpress XLS microscope, and the size of each tiff image is 2160x2160 px. Since most of the image is background (staining nuclei and a viral particles), I opted for the “Background” mode of CorrectIlluminationCalculate. The problem is that the DAPI-stained nuclei are ~100-200 pixels in size, meaning the block size needs to be at least 200 - 250 pixels to ensure that each block contains background pixels. This leads to very blocky correction images.
So, I have the following questions with respect to how to proceed:
Should I simply use a smaller block size and use “all cycles” to generate an illumination average for all the images, or a larger block size and use “each” / “all cycles” ?
How should I balance the block size and the median filter size for smoothing? If I have a block size of 200px, what would be a reasonable filter size for smoothing?
For other channels with smaller objects, is it reasonable to use a smaller block size? Or should I generate an illumination correction image for each channel using the same settings?