SpikeInterface / SpikeInterface/spikeinterface

Problem with changing certain parameters of docker kilosort4 in Spikeinterface

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Python
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Description

Hello, I have been playing around with the parameters of kilosort4 in spikeinterface. I was told that setting the templates_from_data to false might reduce certain types of noise, but I ran into an error using the following code:

params_kilosort4 = {'do_correction': False,  'templates_from_data': False}
sorting_KS4 = si.run_sorter('kilosort4', rec_corrected, folder=output_folder, 
                        docker_image=True, verbose=True, 
                        remove_existing_folder=True,                        
                        **params_kilosort4)

I got an HTTP error 404 after the docker kilosort4 tried to download the spike templates from "https://www.kilosort.org/downloads/wTEMP.npz".

When I used the kilosort4 GUI with 'templates_from_data' set to false, there was no error, and I found the GUI version uses another HTTP to download the templates: https://osf.io/download/6807fb5958b763aae139aa60/

I suspect that the HTTP wasn't updated in the docker version of Kilosort4. The version I am using on docker is spikeinterface/kilosort4-base latest.

If it takes time to fix the docker image, may I ask what might be a good option to install it locally in spikeinterface? As a beginner in Python, I followed the kilosort4 GUI instructions, it worked and used the GPU. But if I just pip install kilosort in conda, I couldn't get the GPU engaged when I ran kilosort4 in spikeinterface using si.run_sorter without using docker_image. Sorry for the naive question.

Thanks in advance!

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the si.run_sorter('kilosort4', ...) path and the spikeinterface/kilosort4-base Docker image, then compare the template download URL used with templates_from_data=False against the GUI URL in the report. Done means the Docker-backed run no longer receives an HTTP 404 when that parameter is disabled.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
data, devops
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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