I am a cellprofiler newbie and I am stuck with the problem of opening tif-files that contain two fluorescence channels as 16-bit greyscale in each single file. I would like to have both channels to use in the pipeline. ColorToGray module seemed to be the nearest to what I was trying but it doesn’t seem to see both channels. The output is just two copies of the first channel. I am attaching the stub of my pipeline and one example image.
Thanks a lot.
Import.cppipe (4.16 KB)
Image stacks are complicated to unpack. We have lots of help here: cellprofiler.org/tutorials/L … movies.pdf
But more succinctly, I started a pipeline for you, attached. Some notes to get going quickly:
(1) Use the Metadata module to “extract from image file headers”. This way you can see what metadata distinguish your frames (in this case it is the “Frame”)
(2) In Names AndTypes, use this info (i.e. Frame) to split out your channels. Screenshot: cl.ly/image/0h3j0r1B363d
I added GrayToColor just for visualization.
Hope that helps!
DLpipe.cppipe (4.38 KB)
excellent. I wouldn’t have thought of that.
Thank you very much
Glad to help.