SpikeInterface / SpikeInterface/spikeinterface-dockerfiles
Kilosort 2 fails on extremely large "spike" trains
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Description
KS2 throws an error when it finds a huge number of spikes:
"Number of spikes before applying cutoff: 36449620",
"----------------------------------------Error using gpuArray/eig",
"EIG did not converge at index = 881672."
There is a very easy fix that doesn't appear in the docker and the docker is the only way to run KS2 on later versions of Ubuntu.
Would it be possible to add a container with a try and catch added to runTemplates.m in order to use the economy decomposition when huge spiketrains are found?
try
[A, B, C] = svdecon(UA);
catch
[A, B, C] = svd(UA,"econ");
end
The economy-size decomposition removes extra rows or columns of zeros from the diagonal matrix of singular values, S, along with the columns in either U or V that multiply those zeros in the expression A = USV'. Removing these zeros and columns can improve execution time and reduce storage requirements without compromising the accuracy of the decomposition.
https://www.mathworks.com/help/matlab/ref/double.svd.html#d126e1780458
I added this issue to the KS2 repo but I don't have much hope of it being incorporated there now that they are focused on KS4+.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by inspecting the v2.0.2 mainLoop/runTemplates.m entry point and the repository's existing Docker files. Verify how the container runs Kilosort 2 for large spike trains, then ensure the requested fallback to economy-size decomposition is included and the container can complete this case without the gpuArray/eig convergence error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, matlab
- Domain
- devops
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100