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

Redish Lab<a href="https://neuromatch.social/@elduvelle_neuro" class="u-url mention" rel="nofollow noopener noreferrer" 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 noreferrer" target="_blank">#NeuroMethods</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> <a href="https://neuromatch.social/tags/SpikeSorting" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SpikeSorting</a> <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener noreferrer" 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 noreferrer" target="_blank">#NeuroMethods</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" 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 noreferrer" 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 😬

El Duvelle NeuroWhat do <a href="https://neuromatch.social/tags/Electrophysiologists" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Electrophysiologists</a> who record raw data from many channels (<a href="https://neuromatch.social/tags/NeuroPixels" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NeuroPixels</a>, <a href="https://neuromatch.social/tags/Hyperdrives" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Hyperdrives</a>…) 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?<a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> <a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NeuroMethods</a> <a href="https://neuromatch.social/tags/DataManagement" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DataManagement</a>

El Duvelle NeuroWhat’s your best guide on extracellular recordings <a href="https://neuromatch.social/tags/waveform" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#waveform</a> shapes to know if you’re recording from soma, axon, dendrite etc.? (Most interested about <a href="https://neuromatch.social/tags/Hippocampus" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Hippocampus</a> of course) <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Electrophysiology</a> <a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NeuroMethods</a>

spikeinterface📢📢📢 <a href="https://fosstodon.org/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a> and <a href="https://fosstodon.org/tags/spikesorting" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#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" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://forms.gle/6dEdeR7sD7u6u8rU8</a>More info on the event webpage: <a href="https://spikeinterface.github.io/spikeinterface-events/spikeinterface-workshop-2024/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://spikeinterface.github.io/spikeinterface-events/spikeinterface-workshop-2024/</a>

El Duvelle NeuroUpping my shuttle-making game with 3D-printed shuttle molds 😁 💪 <a href="https://neuromatch.social/tags/DriveBuilding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DriveBuilding</a> <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Tetrodes</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a>

Moritz NegwerReally cool <a href="https://mstdn.science/tags/lightsheet" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#lightsheet</a> <a href="https://mstdn.science/tags/microscopy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#microscopy</a> 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 <a href="https://mstdn.science/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a> and <a href="https://mstdn.science/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a> too!) Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation Xue et al., preprint on biorxiv, 2024 <a href="https://doi.org/10.1101/2024.01.03.572456" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1101/2024.01.03.572456</a><a href="https://mstdn.science/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mstdn.science/tags/preprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#preprint</a> <a href="https://mstdn.science/tags/tissueclearing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#tissueclearing</a>

kevinboldingAnyone 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. <a href="https://neuromatch.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://neuromatch.social/tags/electrophysiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#electrophysiology</a> <a href="https://neuromatch.social/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a>

Sharena Rice, PhD🧪🧠 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!<a href="https://mastodon.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mastodon.social/tags/electrophysiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#electrophysiology</a> <a href="https://mastodon.social/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a>

Danai RigaHappy & proud to share our latest work with the <a href="https://neuromatch.social/tags/bluespot" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bluespot</a> community, <a href="https://neuromatch.social/tags/locuscoeruleus" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#locuscoeruleus</a> enthusiasts, and anyone else willing to read 😉<a href="https://www.biorxiv.org/content/10.1101/2023.10.16.562534v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2023.10.16.562534v1</a>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 <a href="https://neuromatch.social/tags/NPY" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NPY</a>-expressing neurons, distributed in the pericoerulean space. We showed that peri-LC NPY cells innervate the region, providing <a href="https://neuromatch.social/tags/NPY" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NPY</a> input onto <a href="https://neuromatch.social/tags/noradrenergic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#noradrenergic</a> 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 <a href="https://neuromatch.social/tags/neuromodulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuromodulation</a> of the LC in adaptive behaviors. We re happy to hear your thoughts /ideas /feedback on our data. Please share/boost. Happy reading 🔵<a href="https://neuromatch.social/tags/preprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#preprint</a> <a href="https://neuromatch.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://neuromatch.social/tags/systemsneuro" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#systemsneuro</a> <a href="https://neuromatch.social/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a> <a href="https://neuromatch.social/tags/stress" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#stress</a>

El Duvelle<a href="https://neuromatch.social/@manisha" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@manisha</a> <a href="https://neuromatch.social/@amchagas" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@amchagas</a> <a href="https://neuromatch.social/@jonny" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@jonny</a> thanks! And that sounds like a great idea! I’ll try to make a list of all the <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> techniques that I know of, for which some electronics knowledge would be useful, trying to view it from a completely electronics-naive person. Note: this is for the purpose of what to cover in a future workshop, no need to answer here! Well except if you know about bubble testing ;)These are going to be for tetrodes / probe recordings:Electrodes preparation:<ul><li>what does it mean to stimulate with a positive or negative current</li><li>what is impedance (how does it compare to resistance) and why do we want it to be low, but not too low -what is the solution that best approximates impedance of the brain (eg diluted saline, gold solution,…) </li><li>what happens exactly during gold-plating of the electrodes (or other types of plating) </li><li>what happens if you gold plate too much and get a short, why is it bad, how to fix it </li><li>why does the impedance of your wires usually increase with time after doing a clean cut </li><li>what happens during bubble-testing (some of this is still a mystery even to me): with the electrodes in a saline solution, you send a negative current between the drive pin corresponding to the electrode to test and the solution, if the electrode is properly connected, a small bubble will appear at the tip of the electrode. From experience, the characteristics of the bubble can give you information about the quality of the electrode cut as well as if the electrode is shorted with other electrode, maybe even about the impedance. So what mechanism creates this bubble exactly? Why does the measured impedance just after doing a bubble test might seem very low (sometimes)? Does this really help cleaning the tip of the electrodes? Can it negatively affect the electrode if done for too long or with too high a current? Should the strength of this stimulation current be adjusted depending on the wire diameter? </li><li>when you plate, is it expected that the plated particles will slowly detach with time? How to avoid this? (Either prior to after surgery) </li></ul>Grounding<ul><li>why do you need a ground in in-vivo recordings? </li><li>what is the difference between signals recorded with respect to the ground and “referenced” (ie with respect to another electrode), what is the point of doing both? </li><li>should the ground be connected to any point in the animal, should it be in the skull, should it be above dura, should it be touching the brain? </li><li>could you have two or more ground screws to maximize the changes of having a good animal ground? </li><li>why do you need to ground your recording system properly, why do the characteristics of that ground matter </li><li>why do you sometimes need to also ground your maze / environment, and how </li><li>ground loops when do they happen, what are they, how to detect them, how to avoid them </li></ul>Recordings<ul><li>what tests to do in a newly-implanted animal to make sure that everything works as planned?</li><li>which of these tests can you do with a signal generator instead, what would be the characteristics of that signal so that it mimics brain signals</li><li>why do disconnected channels look the way they look (generally noisy instead of being flat)</li><li>how will the signal change depending on the impedance of the electrodes?</li></ul>Electrolytic lesions<ul><li>what happens when you do an electrolytic lesion (sending a small current between an implanted electrode and the animal ground to create lesions or gliosis in the brain around the electrode that will be visible when you stain the brain to indicate the position of the electrode) </li><li>how does the current amplitude and stimulation duration relate to the size of the lesion </li><li>how would the lesion change if you do a continuous stimulation vs alternating stimulation</li><li>which rules govern where the current “goes” for example if you do the lesion between an electrode and the animal ground but there is also an alternate (maybe lower resistance) route connecting these two points?</li></ul>Okay I’ll send these out before I loose my draft but might add some more later! Where these the kind of questions that you expected? Let me know if any need clarification or even schematics / photos

PLOS Biology.@neurobanks &co describe organization of human neocortex on multiple spatial scales, using resting state intracranial <a href="https://fediscience.org/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a>... hierarchical organization of <a href="https://fediscience.org/tags/AuditoryCortex" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AuditoryCortex</a> & a limbic stream that parallels ventral & dorsal processing streams <a href="https://fediscience.org/tags/PLOSBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PLOSBiology</a> <a href="https://plos.io/44ufoJi" rel="nofollow noopener noreferrer" target="_blank">https://plos.io/44ufoJi</a>

Andy AlexanderAlexander Lab website is now up: <a href="https://alexander.psych.ucsb.edu/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://alexander.psych.ucsb.edu/</a>I am recruiting a grad student through @UCSBpsych this year so if you think you might be a good fit please reach out!<a href="https://neuromatch.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://neuromatch.social/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a> <a href="https://neuromatch.social/tags/neurojobs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neurojobs</a>

Alicia Izquierdo, Ph.D.<a href="https://neuromatch.social/@elduvelle_neuro" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@elduvelle_neuro</a> this is great! I’m curious what you and other <a href="https://neuromatch.social/tags/Electrophysiologists" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Electrophysiologists</a> think of dexamethasone treatment as postop care? It seems a more prevalent practice among those working with <a href="https://neuromatch.social/tags/Neuropixels" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Neuropixels</a> but not amongst the <a href="https://neuromatch.social/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a> community-at-large <a href="https://neuromatch.social/tags/EphysTip" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EphysTip</a> <a href="https://neuromatch.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a>

El Duvelle NeuroMy dream goal on here is to attract enough <a href="https://neuromatch.social/tags/Electrophysiologists" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Electrophysiologists</a> 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 <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> colleagues to join! (Or they can also join the <a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NeuroMethods</a> slack but that’s less fun)

El Duvelle<a href="https://fosstodon.org/@Claudio11" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@Claudio11</a> it’s unrelated to Mastodon - it is a slack platform: <a href="https://neuromethods.slack.com/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://neuromethods.slack.com/</a> (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 <a href="https://neuromatch.social/tags/NeuroMethods" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NeuroMethods</a> 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 <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Electrophysiology</a> people on there!

El Duvelle<a href="https://neuromatch.social/@Raphael_Brito" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@Raphael_Brito</a> Hi and welcome!!! Great to have you on here :) A new addition to my <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> list :)

Susan LDoes anyone have some sort of script for writing neuralynx .NTT files? That would be very helpful<a href="https://neuromatch.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://neuromatch.social/tags/ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ephys</a>

El Duvelle<a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Neuroscience</a> <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ephys</a> question: anyone recognize these signals? The wavy thing? It’s supposedly in rat cortex (above hippocampus), when the rat is immobile, possibly sleepy. Recorded with <a href="https://neuromatch.social/tags/Tetrodes" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Tetrodes</a>. The x-axis scale for each of the two columns is 1s. <a href="https://neuromatch.social/tags/Electrophysiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Electrophysiology</a>

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