I’ve just started to use CellProfiler and I think it is a great tool for automatic segmentation. My images are z-stacks of 4 different channels, where I would like to study colocalization. Thus I’ve downloaded the CP 3.0.0 version and followed the 3D Monolayer tutorial, as well as Colocalization Example in order to have an idea of how to proceed with this type of files.
I have now started with my images, however I have already found a problem. When I drag my images into the file list either they do not have the same appearance as when I open them by FIJI (see attached screenshot) or they look the same as in FIJI in the beginning but in any case (in both cases actually) they look different from the FIJI files when I start applying the different filters. That is to say, the images I want to start processing always have much higher background than my actual images. They are 12 bits images acquired with a confocal Olympus (.oib files) saved as .tiff with FIJI when I split the channels and gray-scale them . This problem happens even if I transform them to 8 bits images beforehand. Can please anyone help me?