No better place to get a hands-on glimpse into the various software tools @ebrains has to offer, Europe's emerging RI for brain research. Choose from over 16 tutorials for software that are already offered, like the EBRAINS Knowledge Graph for data sharing, TVB, and NEST for neural simulation, or Cobrawap for analyzing spatial activity dynamics... And myself -- I will also be there with a tutorial on #ephys data analysis and data handling with Neo. See you there! https://fosstodon.org/@ebrains@mastodon.social/113837231713079532

#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)

@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 😬

What do #Electrophysiologists who record raw data from many channels (#NeuroPixels, #Hyperdrives…) do for data backup and storage? I just bought 2 x 4Tb external drives and it looks like they won’t be enough (at all). Is there a cheap and reliable AND huge storage way to do this?

#Ephys #NeuroMethods #DataManagement

What’s your best guide on extracellular recordings #waveform shapes to know if you’re recording from soma, axon, dendrite etc.? (Most interested about #Hippocampus of course)
#Ephys #Electrophysiology #NeuroMethods

📢📢📢
#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/

Upping my shuttle-making game with 3D-printed shuttle molds 😁 💪
#DriveBuilding #Tetrodes #Ephys

Really cool #lightsheet #microscopy application:

An atlas of the developing mouse brain (DevATLAS from Yongsoo Kim's lab), combined with a new neuronal activity reporter line (Npas4-Cre), shows the order in which brain regions become active in the first postnatal weeks.

(And they have #ephys and #rnaseq too!)

Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation
Xue et al., preprint on biorxiv, 2024
https://doi.org/10.1101/2024.01.03.572456

#neuroscience #preprint #tissueclearing

Anyone know what this artifact is? This is the power spectrum for one channel out of 128 recorded with Neuronexus polytrodes using a Neuronexus Smartbox Pro. That weird regular set of peaks is on every channel. It's at subdivisions of the sampling frequency (30000 Hz). There is ostensibly a hardware antialiasing filter in effect at 15000 Hz. My internet searches have not proved enlightening. #neuroscience #electrophysiology #ephys

🧪🧠 Whole cell patch clamp ephys with this rig, @uofmichigan 2015.

Used a micromanipulator, microscope, and micropipette to measure miniature excitatory postsynaptic potentials in neuronal culture!

Having just the right continuity with the membrane felt like a lunar landing. But on a pyramidal neuron!

#neuroscience #electrophysiology #ephys

#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

Happy & proud to share our latest work with the #bluespot community, #locuscoeruleus enthusiasts, and anyone else willing to read 😉

https://www.biorxiv.org/content/10.1101/2023.10.16.562534v1

4 years ago, we had the idea that endogenous neuromodulatory systems are in place that control LC activity, thereby promoting adaptive behavioral responses in challenging environments.

We examined the role of Neuropeptide Y, as a possible candidate system for this, and identified a new population of #NPY-expressing neurons, distributed in the pericoerulean space.

We showed that peri-LC NPY cells innervate the region, providing #NPY input onto #noradrenergic neurons of the LC, and strongly inhibiting their activity, via Y1Rs.

Next, we showed that chemogenetic stimulation of NPY cells led to anxiety-relief, via Y1Rs, and conversely, inhibition of NPY neurons triggered an anxiogenic phenotype.

Together, we showed a novel role for NPY-mediated #neuromodulation of the LC in adaptive behaviors.

We re happy to hear your thoughts /ideas /feedback on our data.

Please share/boost. Happy reading 🔵

#preprint #neuroscience #systemsneuro #ephys #stress

My #NeuroRat implanted… 7 months ago still has nice clusters!!
#TetrodePower
#Ephys #Neuroscience #Tetrodes #Hippocampus

.@neurobanks &co describe organization of human neocortex on multiple spatial scales, using resting state intracranial #ephys... hierarchical organization of #AuditoryCortex & a limbic stream that parallels ventral & dorsal processing streams #PLOSBiology https://plos.io/44ufoJi

Alexander Lab website is now up:
https://alexander.psych.ucsb.edu/

I am recruiting a grad student through @UCSBpsych this year so if you think you might be a good fit please reach out!

#neuroscience #ephys #neurojobs

@elduvelle_neuro this is great! I’m curious what you and other #Electrophysiologists think of dexamethasone treatment as postop care? It seems a more prevalent practice among those working with #Neuropixels but not amongst the #ephys community-at-large #EphysTip #neuroscience

My dream goal on here is to attract enough #Electrophysiologists so that we can debate things like which drives to use, nichrome or platinum wire, what gold-plating impedance, Vaseline or kwik-sil for surgery, tetrodes in or out of brain, going backwards during screening or not, which is the best recording system, rats vs mice (rats, ofc), etc.

So please tell your #Ephys colleagues to join! (Or they can also join the #NeuroMethods slack but that’s less fun)

@Claudio11 it’s unrelated to Mastodon - it is a slack platform: https://neuromethods.slack.com/
(Have you ever used slack?)

If you have an academic email you could try to create an account with that and it might work, because it has some pre-approved domains.
If that doesn’t work, I’ll be happy to send you an invite link by direct message.

The #NeuroMethods slack is a platform where scientists can ask technical questions to other scientists. In general there will be at least 1 person who can answer your question - although we do need more #Ephys #Electrophysiology people on there!