Try out SpikeInterface pipeline for .ntt data

vandermeerlab / data-formats

Playing around with different data formats and loaders

MIT License

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Try out SpikeInterface pipeline for .ntt data #4

Open mvdm opened 4 years ago

mvdm commented 4 years ago

https://github.com/SpikeInterface seems nice because many loaders and sorters are included.

[ ] Test if we can get this to produce output at all. Yarik has a basic pipeline up and running for .ntt data here: https://github.com/vandermeerlab/data-formats/blob/master/yoh_try_spikeinterfaces.ipynb
[ ] Check out output visualizations (could maybe use CellExplorer)
[ ] Apply it to multiple segments (I did on a single one), see comments and pointers in the notebook
[ ] Find a way to benchmark/compare output with gold standard (e.g. spikeforest, this uses quantitiative metrics)

mvdm commented 4 years ago

@transedward, @CodeWander94 interested in trying this out?

yarikoptic commented 4 years ago

Note: the notebook would still need unreleased versions of libraries.

manimoh commented 4 years ago

@transedward, @CodeWander94 interested in trying this out? I don't mind taking this up. Will go ahead and assign this issue to myself.

manimoh commented 4 years ago

Note: the notebook would still need unreleased versions of libraries.

Looks like the patches are merged into the main release so it was relatively straight forward to make the notebook work. Except for this rather minor aspect:

manimoh commented 4 years ago

I did a bunch of tests on the spikeInterfaces pipeline. I need to do a few more things to be sure, but I think as of now, it can't handle the ntt files. See this notebook for more details.