I’m entirely new to using CellProfiler, so you’ll have to forgive my ignorance. However, I’m trying to set up a process to analyze multiple sets of images (some of which are yet to be collected).
First, I followed the instructions at cellprofiler.org/CPmanual/He … ssing.html to set up the batch files, but those instructions seem to be outdated, in that instead of getting the expected Batch_data.mat file, all I got was a Batch_data.h5 file. According to the help for the CreateBatchFiles module
Has the future already arrived? Do both the web page and the in-module text need to be updated? Note that currently the OutputFilename and Output file format fields of the CreateBatchFiles UI don’t seem to do anything.
Second, I assume I can still use the recommended invocation command of
but substituting Batch_data.h5 as the argument for the -p option. I’m not entirely sure what qualifies as an “Image Set”. What is that?
Finally, I’m unclear on the image specification vs the pipeline specification. I’d like to be able to set up (or have an expert user set up) a pipeline and invoke it against any directory of images, breaking the set of images in the directory up into chunks and feeding chunks to different nodes in our cluster. When next week’s images come in, I’d like to use the same pipeline, but point to a different directory of images. However, it looks like you have to specify the image directory as part of creating the .h5 file, and that requires running the GUI again. Is there a way to re-use a pipeline like this?