I'm a new PhD student and a new user of CellProfiler as well.
I'm trying to measure the intensity of the membrane regions of cell. I have set up a pipeline that 1) recognise cells 2) Shrink several pixels 3) Enlarge several pixels. I create a double ring to overlay the membrane, and measure the intensity in those rings. I attach the pipeline together with a test set of 3 pictures.
Right now I am running the same pipeline on 84 pictures and it takes 48min on my computer (2010 baseline MBP, but that for some reason feels sluggish nowadays). On my colleagues MBP (2012 non-retina baseline, upgraded to 16GB ram and SSD) it takes 26 mins.
If anyone could take a look at my pipeline it would be awesome. I'm sure it's not optimised at all, but it would be great if someone could tell me some specific things that I could change to speed it up.
I am planning a new computer purchase, and faster CellProfiler calculations is one the goals (computer cluster is out of the question for me).
In the Activity Monitor I notice that CellProfiler uses 100% cpu. Is the graphic card and hard drive (would SSD help) also used, or is the cpu the only bottleneck? It "only" uses 100% cpu which also makes me think it only uses one of the cup's. My cpu is 2.4 GHz Intel Core 2 Duo and my colleagues is 2.5GHz Intel Core i5, is this the only reason why his calculations are half the time of mine? Is there any beta that can utilise more cores that I could happily test??
Thanks so much! Loving this program
Greetings from Sweden
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