Cellprofiler nameandtypes error1/5/2024 mkdir cellprofiler-batch-tutorial cd cellprofiler-batch-tutorial We are making these changes because the image is set up in such a way that it is very well suited for a job queue environment, but what we want here is to dig around with some exploratory analysis.Ĭreate a project directory, cellprofiler-batch-tutorial, and cd into it. We will be using the default CellProfiler docker image with a few changes. Here’s a quick explanation and tutorial from Ubuntu to get you started. This does not require too much Linux command line knowledge, but you will need to be able to type commands and navigate a directory structure. Quick disclaimer, if you are very uncomfortable with the command line you may want to reach out for help. Once you have it all set up you treat it just as you would a regular computer. A docker container is like a virtual machine, except without a visual interface. If you prefer to watch, here is a video where I go through the steps described.ĭocker is a way of packaging applications. Here’s a tutorial of step 7, submit your batches to the cluster. The instructions for the CreateBatchFiles module describe how to set up a CellProfiler pipeline and submit it to a cluster. If you need to find a way to decrease your computational resources you can often split your dataset. The larger the dataset you are analyzing the more memory it consumes. This is also an important consideration if you are running out of memory or CPU. You could split that analysis into 4 chunks, and each would complete in 15 minutes. Say you have a large dataset that would take 1 hour to complete. This is helpful when you have a very large dataset. One of the benefits of running CellProfiler in batch is that you can split your analysis. Or not so large scale analyses that you prefer to automate! Running CellProfiler in batch mode is the ideal way to automate large scale analyses.
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