#spikesorting — Public Fediverse posts

What is #neuronalSpiking? Neurons in the brain use electrical signals to communicate with each other and with the body. Each time a neuron is electrically active and this activity exceeds some threshold we can detect this activity as a spike.

Here, we used high-dimensional multielectrode arrays (HD-MEA) with thousands of electrodes, able to measure extracellular electrical potentials of single neurons. The recorded data consisted of raw voltage traces sampled at low frequency of 20 kHz for each of thr 4,096 recording channels. We implemented the reading of these data in #spikeinterface and could reuse the spikeinterface methods to run the spike detection and sorting with #Kilosort.

#SpikeSorting is important because, firstly, neuronal units may span over multiple electrodes, and secondly, an electrode may measure activity from multiple nearby neuronal units. To study biological questions it was essential to measure the spiking activity of real neuronal units instead of electrodes.

What is #neuronalSpiking? Neurons in the brain use electrical signals to communicate with each other and with the body. Each time a neuron is electrically active and this activity exceeds some threshold we can detect this activity as a spike.

Here, we used high-dimensional multielectrode arrays (HD-MEA) with thousands of electrodes, able to measure extracellular electrical potentials of single neurons. The recorded data consisted of raw voltage traces sampled at low frequency of 20 kHz for each of thr 4,096 recording channels. We implemented the reading of these data in #spikeinterface and could reuse the spikeinterface methods to run the spike detection and sorting with #Kilosort.

#SpikeSorting is important because, firstly, neuronal units may span over multiple electrodes, and secondly, an electrode may measure activity from multiple nearby neuronal units. To study biological questions it was essential to measure the spiking activity of real neuronal units instead of electrodes.

What is #neuronalSpiking? Neurons in the brain use electrical signals to communicate with each other and with the body. Each time a neuron is electrically active and this activity exceeds some threshold we can detect this activity as a spike.

Here, we used high-dimensional multielectrode arrays (HD-MEA) with thousands of electrodes, able to measure extracellular electrical potentials of single neurons. The recorded data consisted of raw voltage traces sampled at low frequency of 20 kHz for each of thr 4,096 recording channels. We implemented the reading of these data in #spikeinterface and could reuse the spikeinterface methods to run the spike detection and sorting with #Kilosort.

#SpikeSorting is important because, firstly, neuronal units may span over multiple electrodes, and secondly, an electrode may measure activity from multiple nearby neuronal units. To study biological questions it was essential to measure the spiking activity of real neuronal units instead of electrodes.

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

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

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

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

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)

#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)

#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)

#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)

#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

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

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

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

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.

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

#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 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!

#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

#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

#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

#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!!!

#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!!!

#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!!!

#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!!!

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/

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/

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/

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

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

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