Issues running pipeline


First, thanks for designing such a nice software to reduce the tediousness of manually analyzing images.

I have been designing a new pipeline based on the Speckle Counting example pipeline, that I want to use to measure the number of cells that have speckles and how many speckles each cell has, comparing it to the amount of fluorescence in the red channel.

So far I got the pipeline running in test mode, however I have problems when running it since it will not finish (to analyze 6 images of 4096x4096 pixels the estimated time after running for 24h is more than 70h more - using a 16GB Windows PC in this case). I am not sure why this is happening when running the test mode takes only about 10 minutes.

I also wanted to ask what kind of computer specs are recommended to run pipelines on. I would like to use my work iMac (processor: 2.7 GHz Intel Core i5, memory 8GB 1600 MHz DDR3) but I cannot run it here so far since it always gives me Memory issues, except sometimes when I run it in test mode and “close the eye” on the IdentifyPrimaryObject steps - if not it invariably crashes due to memory issues).

I am currently inputing .czi images that are about 100.7 MB (3 channels). Do you think that making them into a different format (i.e. from 1 image of 4096x4096 pixels to 8 images of 1024x2048 pixels and convert to .tiff) could solve my problem? I am attaching the pipeline to see if you could lend me a hand. I am very eager to use CellProfiler to carry out the analysis of a medium and later a high throughput screening that I am currently setting up.

Thank you in advance.
Rosa_speckle-analysis.cpproj (929.3 KB)