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El Duvelle NeuroThis <a href="https://neuromatch.social/tags/NeuralNet2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuralNet2025</a> conference seems interesting: <a href="https://neuralnet2025.sciencesconf.org/resource/page/id/1" rel="nofollow noopener" translate="no" target="_blank">https://neuralnet2025.sciencesconf.org/resource/page/id/1</a>where: Bordeaux Neurocampus (France) when: Wednesday 26 noon to Friday 28 noon preceded by: minischool on spike sorting (Tuesday 25 - Wed.26).<a href="https://neuromatch.social/tags/NeuralNet" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuralNet</a> <a href="https://neuromatch.social/tags/NeuroConf" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuroConf</a> <a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a>

El Duvelle Neuro<a href="https://neuromatch.social/tags/Tetrode" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrode</a> 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!<a href="https://neuromatch.social/tags/Hexamaze" class="mention hashtag" rel="nofollow noopener" target="_blank">#Hexamaze</a> <a href="https://neuromatch.social/tags/NeuroRat" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuroRat</a> <a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ephys</a> <a href="https://neuromatch.social/tags/Hippocampus" class="mention hashtag" rel="nofollow noopener" target="_blank">#Hippocampus</a> <a href="https://neuromatch.social/tags/PlaceCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#PlaceCells</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> (-related)

El Duvelle NeuroIt's always nice when you finally finish <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> an old recording session and find many <a href="https://neuromatch.social/tags/PlaceCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#PlaceCells</a> (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. <a href="https://neuromatch.social/tags/Hippocampus" class="mention hashtag" rel="nofollow noopener" target="_blank">#Hippocampus</a> <a href="https://neuromatch.social/tags/Neurorat" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neurorat</a> <a href="https://neuromatch.social/tags/Hexamaze" class="mention hashtag" rel="nofollow noopener" target="_blank">#Hexamaze</a>

Redish Lab<a href="https://neuromatch.social/@elduvelle_neuro" class="u-url mention" rel="nofollow noopener" target="_blank">@elduvelle_neuro</a> I don't think it would be possible to record a single neuron on multiple tetrodes. What is the separation between your tetrodes?<a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuroMethods</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ephys</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrodes</a>If you do need cross-correlation code, there is mex'd cross-correlation code in MClust.

El Duvelle Neuro<a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuroMethods</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ephys</a> 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 <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> 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 😬

spikeinterface📢📢📢 <a href="https://fosstodon.org/tags/ephys" class="mention hashtag" rel="tag">#ephys</a> and <a href="https://fosstodon.org/tags/spikesorting" class="mention hashtag" rel="tag">#spikesorting</a> community!We are thrilled to announce the "Tools and Methods for Next Generation Electrophysiology" event, happening in Edinburgh from May 27-31.Registration link: <a href="https://forms.gle/6dEdeR7sD7u6u8rU8" target="_blank" rel="nofollow noopener" translate="no">https://forms.gle/6dEdeR7sD7u6u8rU8</a>More info on the event webpage: <a href="https://spikeinterface.github.io/spikeinterface-events/spikeinterface-workshop-2024/" target="_blank" rel="nofollow noopener" translate="no">https://spikeinterface.github.io/spikeinterface-events/spikeinterface-workshop-2024/</a>

spikeinterface<a href="https://fosstodon.org/tags/NeuroMastodon" class="mention hashtag" rel="tag">#NeuroMastodon</a> <a href="https://fosstodon.org/tags/ephys" class="mention hashtag" rel="tag">#ephys</a> <a href="https://fosstodon.org/tags/spikesorting" class="mention hashtag" rel="tag">#spikesorting</a> 📢📢📢📢📢 SpikeInterface v0.99.0 has been released on <a href="https://fosstodon.org/tags/PyPi" class="mention hashtag" rel="tag">#PyPi</a>!<a href="https://pypi.org/project/spikeinterface/0.99.0/" target="_blank" rel="nofollow noopener" translate="no">https://pypi.org/project/spikeinterface/0.99.0/</a>Just run this to upgrade your installation: >>> pip install --upgrade spikeinterfaceCheck out the release notes here: <a href="https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html" target="_blank" rel="nofollow noopener" translate="no">https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html</a>

Luigi PetruccoSpent a month in procrastination to avoid debugging a horribly patched <a href="https://neuromatch.social/tags/spikesorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#spikesorting</a> pipeline in MATLAB. Then came to discover <a href="https://fosstodon.org/@spikeinterface" class="u-url mention" rel="nofollow noopener" target="_blank">@spikeinterface</a> and now I just want to spend my day plotting filtered traces and quality metrics, everything is just so smooth 😍 People in <a href="https://neuromatch.social/tags/open" class="mention hashtag" rel="nofollow noopener" target="_blank">#open</a> neuroscience software are pulling out truly amazing things!

El Duvelle Neuro<a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener" target="_blank">#NeuroMethods</a> poll: which is your favourite manual <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> (refinement) program?🧠🖥️Polls don’t have enough options so detailed answers would be great 😃:1: <a href="https://neurosuite.sourceforge.net/" rel="nofollow noopener" target="_blank">Klusters</a> 2: <a href="https://github.com/adredish/MClust-Spike-Sorting-Toolbox" rel="nofollow noopener" target="_blank">Mclust</a> 3: <a href="https://plexon.com/products/offline-sorter/" rel="nofollow noopener" target="_blank">Offline Sorter</a> 4: <a href="https://phy.readthedocs.io/en/latest/" rel="nofollow noopener" target="_blank">Phy</a> 5: <a href="https://neuralynx.fh-co.com/research-software/spikesort-3d/" rel="nofollow noopener" target="_blank">Spike Sort 3D</a> 6: <a href="http://www.axona.com/index.php" rel="nofollow noopener" target="_blank">Tint</a> (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)

Claudio BasileIs anyone in the neuroscience field using kilosort 3 through spike interface available to help me with some issues/questions? I am currently trying to set up a pipeline using SpikeInterface but am running through some issues. <a href="https://fosstodon.org/tags/spikeinterface" class="mention hashtag" rel="tag">#spikeinterface</a> <a href="https://fosstodon.org/tags/kilosort" class="mention hashtag" rel="tag">#kilosort</a> <a href="https://fosstodon.org/tags/spikesorting" class="mention hashtag" rel="tag">#spikesorting</a> <a href="https://fosstodon.org/tags/mountainsort" class="mention hashtag" rel="tag">#mountainsort</a> <a href="https://fosstodon.org/tags/neuroscience" class="mention hashtag" rel="tag">#neuroscience</a> <a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="tag">#Python</a> <a href="https://fosstodon.org/tags/programming" class="mention hashtag" rel="tag">#programming</a>

El DuvelleA bottle in the sea but has anyone here ever coded a plug-in for <a href="https://neuromatch.social/tags/Phy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Phy</a> (the <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> 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? <a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://neuromatch.social/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#Python</a>

El Duvelle<a href="https://www.biorxiv.org/content/10.1101/2023.06.29.546882v1" rel="nofollow noopener" target="_blank">A modular approach to handle in-vivo drift correction for high-density extracellular recordings</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Electrophysiology</a> <a href="https://neuromatch.social/tags/Probes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Probes</a>

El Duvelle<a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> question: Say I would like to use <a href="https://neuromatch.social/tags/Klustakwick" class="mention hashtag" rel="nofollow noopener" target="_blank">#Klustakwick</a> (3) - I have the .exe of it - with <a href="https://neuromatch.social/tags/SpikeInterface" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeInterface</a> , 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… 🙏

El DuvelleSpike-sorting, before /afterThis uses the automated method Klustakwick and then some manual refinement<a href="https://neuromatch.social/tags/PlaceCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#PlaceCells</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrodes</a> <a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a>

El Duvelle<a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> : 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: <a href="https://phy.readthedocs.io/en/latest/" rel="nofollow noopener" target="_blank">https://phy.readthedocs.io/en/latest/</a>) *Edit: added these hashtags: <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Electrophysiology</a> <a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrodes</a> *

spikeinterface<a href="https://fosstodon.org/tags/NeuroMastodon" class="mention hashtag" rel="tag">#NeuroMastodon</a> <a href="https://fosstodon.org/tags/ephys" class="mention hashtag" rel="tag">#ephys</a> <a href="https://fosstodon.org/tags/spikesorting" class="mention hashtag" rel="tag">#spikesorting</a>SpikeInterface v0.97.0 has been released on <a href="https://fosstodon.org/tags/PyPi" class="mention hashtag" rel="tag">#PyPi</a>: <a href="https://pypi.org/project/spikeinterface/" target="_blank" rel="nofollow noopener" translate="no">https://pypi.org/project/spikeinterface/</a>Just run: >>> pip install --upgrade spikeinterfaceThe new release includes several new features and updates to the package! A detailed list of changes can be found here: <a href="https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.html" target="_blank" rel="nofollow noopener" translate="no">https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.html</a>Happy <a href="https://fosstodon.org/tags/spikesorting" class="mention hashtag" rel="tag">#spikesorting</a> to everyone!!!

El DuvelleHi, is anyone using <a href="https://neuromatch.social/tags/Mountainsort" class="mention hashtag" rel="nofollow noopener" target="_blank">#Mountainsort</a> with <a href="https://neuromatch.social/tags/Neuralynx" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuralynx</a> data? Are you using <a href="https://neuromatch.social/tags/SpikeInterface" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeInterface</a> to convert the input data? Would you share your code? 😃🙏 <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a>

El Duvelle2/ Here are some interesting tables from it... I wonder how well it works with <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrodes</a> and in the <a href="https://neuromatch.social/tags/Hippocampus" class="mention hashtag" rel="nofollow noopener" target="_blank">#Hippocampus</a> given the special shape of <a href="https://neuromatch.social/tags/ComplexSpikes" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComplexSpikes</a> 🤔If you try it please let us know what you think!!<a href="https://neuromatch.social/tags/Kilosort" class="mention hashtag" rel="nofollow noopener" target="_blank">#Kilosort</a> <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Electrophysiology</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> 2/

El DuvelleLooks like <a href="https://neuromatch.social/tags/Kilosort" class="mention hashtag" rel="nofollow noopener" target="_blank">#Kilosort</a> 4 is out! <a href="https://www.biorxiv.org/content/10.1101/2023.01.07.523036v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.01.07.523036v1</a>If you're doing spike-sorting for your research... are you going to try it out?<a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Electrophysiology</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> 1/ some screenshots below

El Duvelle<a href="https://neuromatch.social/@chrisXrodgers" class="u-url mention" rel="nofollow noopener" target="_blank">@chrisXrodgers</a> 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: <a href="https://github.com/elduvelle/SpikeinterfaceMS4_GenzelLab" rel="nofollow noopener" target="_blank">https://github.com/elduvelle/SpikeinterfaceMS4_GenzelLab</a>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! <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeSorting</a> <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrodes</a> <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Electrophysiology</a>

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