Cell Profiler Knime Integration

#1

Hi Everyone,

I am new to knime and have been trying to utilize the knime extensions that integrate cell profiler pipelines. I have it working and it does run through the cell profiler pipeline properly, however, it is much slower than using cell profiler alone. Upon investigation, it appears to me that when knime uses cell profiler it does not utilize all of my computers cores, rather it just uses one. That being said, I was wondering if there was anyway to have knime cell profiler use close to or at 100 percent of my cpu. It may be as simple as a setting I am missing, thank you.

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#2

Hi @ReidF,

It is actually not that easy. Although I am not entirely sure, I’d assume that CellProfiler’s CPU utilization stems from the fact that they are processing multiple images in parallel. Since we feeding images row-by-row to CellProfiler that is not a lot that can be parallelized.

You could try to wrap the CellProfiler Pipeline Executor in a Parallel Chunk Start and Parallel Chunk End to enforce the parallelization on KNIME side. Let me know how it goes!

Best,
Stefan

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