CaImAn and named-pipes (for IPC)

[ttompost]

• Tell us a bit about your setup:

  1. Operating system (Linux/macOS/Windows): Windows 10 Professional

  2. Python version (3.x): Python 3.7

  3. Working environment (Python IDE/Jupyter Notebook/other): PyCharm IDE

  4. Which of the demo scripts you're using for your analysis (if applicable): online OnACID (or VolPy - if it can provide online analysis (see my question below))

  5. CaImAn version*: CaImAn 1.8.1

  6. CaImAn installation process (pip install ./pip install -e ./conda): via Miniconda3

*You can get the CaImAn version by creating a params object and then typing params.data['caiman_version']. If the field doesn't exist, type N/A and consider upgrading)

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Dear CaImAn developers/community,

rather than having an issue, I would like to ask for an advice on setting up one of CaImAn's online algorithms in a direct inter-process communication (IPC) via named-pipe with another open-source software. CaImAn's documentation page recommends using tiff/hdf5/h5 types of files as input, my question is - should a named-pipe follow the same rule or is another data format suitable to be used?

In addition, I can not find the information whether Volpy can perform online analysis of streaming data?

Any help/advice is kindly appreciated.

Best, Tea

[agiovann]

Dear Tea, I am working on something very similar. I think it should come out in a few months. We are connecting to scanimage.

[epnev]

@thethea The short answer is that the CaImAn codebase cannot do this out of box, but can be modified to do it (although that's not a trivial amount of work). Also VolPy cannot work in an online mode at the moment.