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).
#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.
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/
Informatics Forum, University of Edinburgh Workshop 27-28th May 2024 Hackathon 29-31st May 2024 Please contact Matthias Hennig ([email protected]) if you need an invitation letter for visa purposes.
#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
#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)
Robert Wolff
El Duvelle Neuro
Redish Lab
spikeinterface
Luigi Petrucco