Access to arbitrary metadata in Omero

i am getting started with Omero and CP and am trying to build a semi-automated pipeline.

i intend to store global key/value pairs for intensity maxima and minima (calculated using all files of a given wavelength) in Omero, and would like to use these values as inputs to certain CP modules. does CP’s Omero integration allow this?

i assume another way is to query the data from Omero myself on the command line and insert these values into the CP pipeline file (it’s all new to me)

thanks in advance for any tips!

AFAIK, only a few certain pieces of metadata are currently pulled- Plate, Well, Site, Channel, number of Z planes, number of time points, and I thiiiink that’s it. You could probably alter the code of the Omero integration module to pull more metadata columns, and CP is definitely capable of using metadata to do things like set thresholds and rescale images, but depending on how many batches you have, how many places the metadata needs to be changed from batch to batch, and your own comfort with scripting it’s difficult to say whether manually querying the information or rewriting the module would be easier.

thank you for the response! i am comfortable with scripting. i will be using CP headless, so i basically need to inform the pipeline about these values - is there an established way to pass such arguments or edit a copy of a .cpproj file?

If you’re going to be running headless, you’ll be passing a file list in either text or CSV format alongside a .cppipe file; the cppipe is essentially just a text file with the list of operations to do, so I believe you should be able to easily edit it with a script to change the rescale or thresholding values you want.

More tips and tricks for running headless are at this page here on our wiki.

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