SpikeInterface / SpikeInterface/spikeinterface
Problem with changing certain parameters of docker kilosort4 in Spikeinterface
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 847
- Forks
- 280
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 29
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!
Contributor guide
No contributing guide indexed for this repository
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 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