I apologise for bothering. I am a beginner in using CellProfiler and my question seems to be quite "stupid", because I have an issue with Maximum Intensity projection. I took images of my cells in three channels, ten Z-positions, and several positions in the well. These images are saved separately in tiff format. My aim is to make Z-stack projection of individual channels in individual well positions.
I have prepared a pipeline where I identified each channel and grouped data based on well positions in "Groups". When I launched the pipeline in "Start Test Mode", I saw only the first image of whole channel set after MakeProjection. Not Z-stack projection. When the pipeline contained SaveImages and I launch it in "Analayze Images", I saw only the last image of the set in output folder in the end of the analysis.
I tried to make maximum intensity projection in ImageJ and it worked. Nevertheless, I have a huge dataset of images which I need analyse, and I want to use CellProfiler.
I also add several pictures of my shorten pipeline and images.
Could anybody refer me to any manual or show me where I did the mistake?
Thank you in advance.