Import and split multi-page tifs

Dear Board,
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.
Christian


Import.cppipe (4.16 KB)

Hi,

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”)
Screenshot: cl.ly/image/0M2r1Q1Q3U44
(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!
David
DLpipe.cppipe (4.38 KB)

Dear David
excellent. I wouldn’t have thought of that.
Thank you very much
Christian

Glad to help.
Cheers,
David