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full bombcell pipeline example with exposed native parameters#4463

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Julie-Fabre wants to merge 19 commits intoSpikeInterface:mainfrom
Julie-Fabre:bombcell_example
Open

full bombcell pipeline example with exposed native parameters#4463
Julie-Fabre wants to merge 19 commits intoSpikeInterface:mainfrom
Julie-Fabre:bombcell_example

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@Julie-Fabre
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@Julie-Fabre Julie-Fabre commented Mar 23, 2026

Adds full bombcell pipeline example with exposed native parameters, unitrefine integration, and upsetplot-bombcell dependency. Work in progress.

Adding:

  • Bombcell example script demonstrating the full pipeline, including configurable parameters and how to modify them.

    • This required changes to expose all parameters available in native bombcell: options to enable/disable drift and distance metrics, choice of RPV calculation method, time chunks etc.
    • adds two wrapper scripts to streamline and make parameters very apparent / easy to modify
    • Updates docs (need to check new refs for template metrics - are they all correct?)
  • Switch to upsetplot-bombcell in place of upsetplot.

@chrishalcrow
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chrishalcrow commented Mar 23, 2026

Hello, looks great. Just to say, we can have docs where you run everything locally, then upload the results. I think this is the only example: https://spikeinterface.readthedocs.io/en/stable/how_to/drift_with_lfp.html
I think it could be a good fit for this case, cause you could actually run a full pipeline from scratch (maybe on data that's available on DANDI) and discuss the results that come out.
EDIT: https://spikeinterface.readthedocs.io/en/stable/how_to/handle_drift.html another!

@Julie-Fabre
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Thanks a lot, Chris! I love that idea. I am going to work on finding a good example dataset and document a nice script describing outputs etc. That's a longer thing to do, so I'll do a separate PR soon.
For now, I think this is ready for review. Let me know what you think! In particular, I added citation info in template metric docs in references.rst. Could you check whether that looks good?

@Julie-Fabre Julie-Fabre marked this pull request as ready for review March 26, 2026 20:26
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