I am trying to measure the mean cytoplasmic signal intensity using a simple pipeline for human cells in CellProfiler (http://www.cellprofiler.org/examples.shtml). However the data points I get using this pipeline do not include the mean signal intensity or any other kind of intensity measurement, instead things like AreaShapeCompactness or AreaShapeSolidity are calculated. How do I modify the pipeline so that it will include mean signal intensity as a data point? I am new to the CellProfiler software and appreciate any help.
Are you including the module MeasureObjectIntensity? It has to come after any primary or secondary object identification. Here's some info from the manual:
http://www.cellprofiler.org/CPmanual/MeasureObjectIntensity.html
Let me know if this helps. I'd be happy to help put together a pipeline with some more info on what your sample images are.
Dear Jordan, thank you so much for your message. I was able to fix the pipeline and to measure the mean intensity per cell. I am analyzing images of fibroblasts which are anything but round what makes it more difficult I guess.
Thank you!
Darius
I know this an old thread and am not sure if you are still working in this area, but I would defintely recommend you visit www.MIPAR.us.
It is very powerful and intuitive 2D/3D image analysis software written by scientists/end-users and is about to be released as a free trial on December 14th. It offers much of the same high-throughput automation as Cell Profiler, but is much more engaging and interactive (when you need it). Just thought I'd recommend!
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