I just discovered CP and want to use it for the scratch wound assay to measure scratch area. I tried to use the example but keep getting a memory error. I converted the supplied .JPG images to .TIF but still get memory error. If I can’t even get past the example it doesn’t give me much confidence for using my own data! Why does the memory error occur?
Sorry for the delay in reply! I believe we have recently restructured the pipeline so that only one image is loaded at a time, which should reduce the memory load. If you use the example pipeline fresh from the Examples website, do you still encountering this error? If so, how much memory does your computer have? For general memory issues, let me refer you to this entry in our FAQ.
hello, i am trying to analyze my scratch wound assay images with cell profiler. but, i cannot use measure area module with my image. it says it needs binary files to do this. dou you have any suggestions for wound analysis pipelines other than measure area? thank you.
It probably better to figure out why you are getting this error to begin with. If you are using the “binary image” option in MeasureImageAreaOccupied, you can create a binary image from a grayscale image by using the ApplyThreshold module in the pipeline. Alternately, you can use the “Objects” option in MeasureImageAreaOccupied, and use an object that you have identified with the IdentifyPrimaryObjects module.