#spikesorting — Public Fediverse posts

This #NeuralNet2025 conference seems interesting:
https://neuralnet2025.sciencesconf.org/resource/page/id/1

where: Bordeaux Neurocampus (France)
when: Wednesday 26 noon to Friday 28 noon
preceded by: minischool on spike sorting (Tuesday 25 - Wed.26).

#NeuralNet #NeuroConf #Neuroscience #SpikeSorting

#Tetrode recordings (in a bundle): did you know that you could record the same neuron on two different tetrodes?
or even three different tetrodes??

After checking that, turns out I usually have about 5-10% of neurons that are a duplicate of another neuron, in a given 8-tetrodes recording! They are pretty easy to detect with a firing rate correlation so I can remove them from analysis.
But I bet most neuron counts in published papers are inflated of that much!

Here's an example where you can see the spike plots and waveforms of 3 different, well-isolated clusters, recorded from 3 different tetrodes!

#Hexamaze #NeuroRat #Neuroscience #Ephys #Hippocampus #PlaceCells #SpikeSorting (-related)

It's always nice when you finally finish #SpikeSorting an old recording session and find many #PlaceCells (here, 101) 🥰

I also recently implemented a way to remove putative duplicate recordings (when spikes from the same neutron are detected in two different tetrodes) and there can be a surprisingly high amount, 6-10 % of cells as far as I can see, this is with bundles of 8 tetrodes.

#Hippocampus #Neurorat #Hexamaze

@elduvelle_neuro

I don't think it would be possible to record a single neuron on multiple tetrodes. What is the separation between your tetrodes?

#NeuroMethods #Ephys #SpikeSorting #Tetrodes

If you do need cross-correlation code, there is mex'd cross-correlation code in MClust.

#NeuroMethods #Ephys what is the fastest way to detect potential duplicate neurons after spike-sorting?
Say you’ve recorded from multiple neurons that might be detected by multiple tetrodes, you do #SpikeSorting per tetrode, and want to detect those duplicates afterwards?

I was thinking cross-correlation across all cell pairs. But my implementation is really slow. If anyone already has code for this (Matlab or Python) I’d be happy to steal it 😬

📢📢📢
#ephys and #spikesorting community!

We are thrilled to announce the "Tools and Methods for Next Generation Electrophysiology" event, happening in Edinburgh from May 27-31.

Registration link:
https://forms.gle/6dEdeR7sD7u6u8rU8

More info on the event webpage:
https://spikeinterface.github.io/spikeinterface-events/spikeinterface-workshop-2024/

#NeuroMastodon #ephys #spikesorting

📢📢📢📢📢
SpikeInterface v0.99.0 has been released on #PyPi!

https://pypi.org/project/spikeinterface/0.99.0/

Just run this to upgrade your installation:

>>> pip install --upgrade spikeinterface

Check out the release notes here:
https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html

Spent a month in procrastination to avoid debugging a horribly patched #spikesorting pipeline in MATLAB. Then came to discover @spikeinterface and now I just want to spend my day plotting filtered traces and quality metrics, everything is just so smooth 😍​
People in #open neuroscience software are pulling out truly amazing things!

#NeuroMethods poll: which is your favourite manual #SpikeSorting (refinement) program?🧠🖥️

Polls don’t have enough options so detailed answers would be great 😃:

1: Klusters
2: Mclust
3: Offline Sorter
4: Phy
5: Spike Sort 3D
6: Tint (I didn't find a link describing the software)
7: Other
8: None (all automatised!)

(Note: I asked the same poll on the NeuroMethods SpikeSorting channel)

A bottle in the sea but has anyone here ever coded a plug-in for #Phy (the #SpikeSorting visualization software)? If yes I have questions for you, like… would you share your plug-in with me so I can see how you did it?
#Neuroscience #Python

A modular approach to handle in-vivo drift correction for high-density extracellular recordings
#SpikeSorting #Electrophysiology #Probes

#SpikeSorting question:
Say I would like to use #Klustakwick (3) - I have the .exe of it - with #SpikeInterface , to pre-sort my spikes. But it is not implemented in the available “sorters”.
“Klusta” is, which seems somewhat similar (made by the same people?) but also quite different. I really like Klustakwick and would just like to try that.
Any ideas?
Where is the best place to ask questions about SpikeInterface? I feel like opening an Issue on the GitHub is a bit overkill… 🙏​

Spike-sorting, before /after

This uses the automated method Klustakwick and then some manual refinement

#PlaceCells #SpikeSorting #Tetrodes #Neuroscience

#SpikeSorting : where would be the best place (or handle / hashtag) to ask questions about Phy? 🙏​
And if you use it, can you let me know, maybe we can help each other?
(This Phy: https://phy.readthedocs.io/en/latest/)
*Edit: added these hashtags: #Electrophysiology #Neuroscience #Tetrodes *

#NeuroMastodon #ephys #spikesorting

SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/

Just run:
>>> pip install --upgrade spikeinterface

The new release includes several new features and updates to the package! A detailed list of changes can be found here:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.html

Happy #spikesorting to everyone!!!

Hi, is anyone using #Mountainsort with #Neuralynx data? Are you using #SpikeInterface to convert the input data? Would you share your code? 😃​🙏​
#SpikeSorting

2/
Here are some interesting tables from it...
I wonder how well it works with #Tetrodes and in the #Hippocampus given the special shape of #ComplexSpikes 🤔​

If you try it please let us know what you think!!

#Kilosort #Electrophysiology #SpikeSorting
2/

Looks like #Kilosort 4 is out!
https://www.biorxiv.org/content/10.1101/2023.01.07.523036v1

If you're doing spike-sorting for your research... are you going to try it out?

#Electrophysiology #SpikeSorting
1/ some screenshots below

@chrisXrodgers
Very good question!
I have most recently used MountainSort + Phy (via SpikeInterface) and I quite like Phy (for manual refinement of clusters) but not so much Mountainsort - it seemed very conservative. I’ll go back to it soon and tweak the settings a bit. If you want to try it out we have some shared code with the Genzel lab here: https://github.com/elduvelle/SpikeinterfaceMS4_GenzelLab

But I was also going to try out Kilosort. Do you really not like it?
Before that KlustaKwik + Tint has been the gold standard for me :) … but maybe it’s time to move on!
#SpikeSorting #Tetrodes #Electrophysiology

#spikesorting #electrophysiology

Happy new year from the SpikeInterface team! 🥳
2023 will be full of updates and new exciting features!

If you'd like to support us and broaden the SI community, please add a ⭐️ to our GitHub page 🙏:
https://github.com/SpikeInterface/spikeinterface

#introduction

SpikeInterface is an #opensource framework in #python to analyze extracellular electrophysiology #ephys data and perform #spikesorting.

We believe that spike sorting development should be a collaborative and community effort and we encourage contributors!

You can read more in the docs:
https://spikeinterface.readthedocs.io/en/latest/

Follow a tutorial:
https://github.com/SpikeInterface/spiketutorials

Check out the source code:
https://github.com/SpikeInterface/spikeinterface/

Happy #spikesorting to all!