Hello helpful people,
Since replacing the "AxioVision" software that controls our Zeiss scope with the newer "Zen" software, I've been encountering the following problem when trying to process my images using the same pipeline that previously worked:
The image that was collected from the blue channel, my DAPI staining, is being assigned to the "Red Channel" in CellProfiler. Similarly, the actual red image is being assigned to "blue channel". This all happens in the ColorToGrey step. I could swap the names on my downstream processing i.e. calling my Red channel the DAPI channel, but that could get confusing and leaves me concerned as to what is going on to cause the issue in the first place.
I've uploaded a zip with my pipeline, an example folder of images that should just be dragged into the images file list and then filtered by clicking "apply filters to list". There is also a screenshot of the result of the ColortoGrey step showing a faintly stained cell body in the "Blue Image" channel and DAPI staining in the "Red Channel"
Thanks in advance!
Help.zip (8.4 MB)