Why am I unable to detect spikes and only noise?

[Auxcy1ene]

Hi there,

I am a masters student at the University of Exeter studying Natural Sciences. I am currently working on my masters project in which I am comparing MEA recordings of healthy recordings and diseased recordings and investigating how the models for each differ, using the model laid out in the paper by Zaytsev et al.: https://pmc.ncbi.nlm.nih.gov/articles/PMC4493949/pdf/10827_2015_Article_565.pdf.

I am using kilosort to detect spikes in my data before feeding it into the modelling code. After a while I was finally able to get kilosort to process my data. Little did I know that at that time although kilosort gui had completed without any software error, the number of clusters detected was far fewer than expected. Only three were detected originally and the recordings were a 4x4 electrode array recording between 50 to 100 neurons. I have been able to increase the number of clusters detected to around 17 by tweaking the kilosort settings, but then I realised another problem.

When viewing the results in phy I realised that the spike waveforms were not actually spikes, it appeared that all the spikes in each cluster were not spikes. I don’t know if noise is the right term for them but they were all just slightly different zigzags. I have uploaded a picture below for reference.

My question is what is going wrong here? Is the issue with the parameters I have selected in kilosort, or is there an error somewhere in the pipeline whereby the raw recordings, in axion biosystems format, are extracted in matlab and then written to a nwb file in python. Another possible source of the error could be the step where the nwb file is converted to a binary file to facilitate use with kilosort gui.

I will a link to a zip folder containing the kilosort results, alongside the recordings at different stages of processing in case that can help anyone isolate the source of the issue.

https://drive.google.com/file/d/1zV2lamdQ0E5tIWg_jgTOvUzG52A6K6Kz/view?usp=sharing

If anyone can help me resolve this issue I would really appreciate it. Also have a happy Christmas.

Many Thanks,

From Sean.H

[jacobpennington]

Can you please upload kilosort4.log from the results directory separately in a comment? A screenshot of the KS4 GUI with your data loaded would also be helpful. You don't need to run the sorting again, just open it and click "load."

[Auxcy1ene]

Will do. Not at my desk at the moment but I'll see if I can do it remote from my phone.

[Auxcy1ene]

here is the link to the kilosort.log. I was unable to upload the file as I couldn't download it to my phone. Also here is a screenshot of kilosort gui with the same data loaded.

[Auxcy1ene]

https://drive.google.com/file/d/19pwwptO6neo5Mb7NgX2IB134REgpnYGl/view?usp=drivesdk sorry the link didn't work in the last comment.