Thanks also for this reply. I have gone ahead and implemented an illumination correction algorithm, and corrected a fairly pronounced parabolic non-uniformity in my images. I agree that this is an important step that will allow better control over further processing steps.
But I have a further question concerning the ‘Adaptive’ option. It is a somewhat technical question, but I think it can be readily answered. In the manual entry for IdentifyPrimaryAutomatic, it states that “Adaptive: the threshold varies across the image”, without any further details. I would like to know if the “Adaptive” option implements a unique threshold for each cell, or if the segmentation thresholds between different cells are still related under the “Adaptive” algorithm.
One reason for this question is a few of my images have large, bright, saturated artifacts. I am wondering if using the “Adaptive” option will allow cells outside of the artefact region to be segmented properly, despite the presence of a large local distortion elsewhere. A second reason is that I am interested in studying the variability of metrics over cells. Thus I would like to have an idea of the possible effect of segmentation on the cell-to-cell variability.
Thanks a lot once again,