Kilosort 2 fails on extremely large "spike" trains
还没有人认领这个 Issue。
评估
调研方向
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.
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描述
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+.
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SpikeInterface/spikeinterface-dockerfiles 的其他 Issue
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docker, kilosort4, blackwell可能已有人在做 @alejoe91 于 159 天前认领。 未关闭
SpikeInterface/spikeinterface-dockerfiles#91 · 已指派 1 人 ·
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难度 4/5 3-5 天 新手友好度 35/100
SpikeInterface/spikeinterface-dockerfiles#89 · 2 条评论 ·
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难度 3/5 1-2 天 新手友好度 25/100
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难度 5/5 一周以上 新手友好度 25/100
SpikeInterface/spikeinterface-dockerfiles#75 · 1 条评论 ·
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难度 4/5 3-5 天 新手友好度 25/100
查看 SpikeInterface/spikeinterface-dockerfiles 的全部 Issue
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