Problem with changing certain parameters of docker kilosort4 in Spikeinterface

[NeuronQi]

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!

[alejoe91]

Hi @NeuronQi

Yep we stumbled upon this as well: MouseLand/Kilosort#932

I'm udated the KS4 image to 4.0.38 and pushed it to dockerhub: SpikeInterface/spikeinterface-dockerfiles#86

Can you check that is's fixed?

[NeuronQi]

Hi @alejoe91, thanks a lot for looking into this and pushing the newer version of KS4 image. I installed the 4.0.38 version, and deleted the older version in docker desktop. However, when I ran the same 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 found the output "Docker: pulling image spikeinterface/kilosort4-base" was taking a long time to run, while in the docker desktop, the older version of kilosort4-base (created 3 months ago but with the tag"latest") re-appeared and got used. Thus, there was still the same HTTP error. Maybe the default is set to using certain version of the KS4 docker image?

Please see my screen shots of the two KS4 docker images attached.
Thanks again!