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scratchrealm / neurobass

Neurobass is a prototype of a web application for managing and running neuroscience analyses.
Apache License 2.0
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integrate SpikeInterface #1

Open bendichter opened 1 year ago

bendichter commented 1 year ago

It would be great to see one of these docker files integrated, particularly kilosort 3, which requires a GPU.

magland commented 1 year ago

I got kilosort3 to work! In a singularity container with a slurm job on our cluster.

Here's the workspace for testing the sorters. If you drill down, you'll be able to see the console output of the job, including elapsed time https://neurobass.vercel.app/workspace/eeisukgs

Here's the raster plot https://flatironinstitute.github.io/neurosift/?p=/nwb&url=https://neurosift.org/neurobass-dev/cdcabb41.nwb&tab=view:DirectRasterPlot|/units

I am using the SpikeInterface docker file (spikeinterface/kilosort3-compiled-base) but I am not using the run_sorter function. Instead I am running the ks3_compiled binary directly in the container without installing SpikeInterface inside the container. I think this is a more robust method and better for reproducibility.

I am not able to test the docker method because I don't have a machine with both docker and GPU. I guess that would be the AWS instance.

So I don't have much experience with AWS, but I think the next step would be to create an AMI that has docker and neurobass - plus the spikeinterface/kilosort3-compiled-base image already pulled. Then we'll need to figure out how to launch with a job task.

bendichter commented 1 year ago

@luiztauffer this seems like a place where you have some experience

magland commented 1 year ago

@luiztauffer this seems like a place where you have some experience

I created a separate issue for deploying to AWS https://github.com/scratchrealm/neurobass/issues/5