#ephys — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #ephys, aggregated by home.social.
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"Phase-specific premotor inhibition modulates leech rhythmic motor output", Martina Radice et al. 2025
https://elifesciences.org/reviewed-preprints/104921 -
"Phase-specific premotor inhibition modulates leech rhythmic motor output", Martina Radice et al. 2025
https://elifesciences.org/reviewed-preprints/104921 -
"Phase-specific premotor inhibition modulates leech rhythmic motor output", Martina Radice et al. 2025
https://elifesciences.org/reviewed-preprints/104921 -
"Phase-specific premotor inhibition modulates leech rhythmic motor output", Martina Radice et al. 2025
https://elifesciences.org/reviewed-preprints/104921 -
"Phase-specific premotor inhibition modulates leech rhythmic motor output", Martina Radice et al. 2025
https://elifesciences.org/reviewed-preprints/104921 -
#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)
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#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)
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#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)
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#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)
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#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)
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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.
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#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 😬
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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?
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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/6dEdeR7sD7u6u8rU8More 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 -
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
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🧪🧠 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!
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#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 v0.99.0 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 🔵
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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 🔵
-
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 🔵
-
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 🔵
-
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 🔵
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CW: Long post about electronics and electrophysiology links
@manisha @amchagas @jonny
thanks! And that sounds like a great idea!I’ll try to make a list of all the #Ephys 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:
- what does it mean to stimulate with a positive or negative current
- 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,…) - what happens exactly during gold-plating of the electrodes (or other types of plating)
- what happens if you gold plate too much and get a short, why is it bad, how to fix it
- why does the impedance of your wires usually increase with time after doing a clean cut
- 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?
- when you plate, is it expected that the plated particles will slowly detach with time? How to avoid this? (Either prior to after surgery)
Grounding
- why do you need a ground in in-vivo recordings?
- 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?
- 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?
- could you have two or more ground screws to maximize the changes of having a good animal ground?
- why do you need to ground your recording system properly, why do the characteristics of that ground matter
- why do you sometimes need to also ground your maze / environment, and how
- ground loops when do they happen, what are they, how to detect them, how to avoid them
Recordings
- what tests to do in a newly-implanted animal to make sure that everything works as planned?
- 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
- why do disconnected channels look the way they look (generally noisy instead of being flat)
- how will the signal change depending on the impedance of the electrodes?
Electrolytic lesions
- 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)
- how does the current amplitude and stimulation duration relate to the size of the lesion
- how would the lesion change if you do a continuous stimulation vs alternating stimulation
- 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?
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
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My #NeuroRat implanted… 7 months ago still has nice clusters!!
#TetrodePower
#Ephys #Neuroscience #Tetrodes #Hippocampus -
My #NeuroRat implanted… 7 months ago still has nice clusters!!
#TetrodePower
#Ephys #Neuroscience #Tetrodes #Hippocampus -
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
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@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
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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)
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@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!
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@Raphael_Brito Hi and welcome!!! Great to have you on here :) A new addition to my #Ephys list :)
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First post, talking to the void: looking to connect with fellow neuroscientists, interested in all things #stress, #locuscoeruleus #neuropeptides #ephys Particularly invested in dialogue, open science & equity
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First post, talking to the void: looking to connect with fellow neuroscientists, interested in all things #stress, #locuscoeruleus #neuropeptides #ephys Particularly invested in dialogue, open science & equity
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First post, talking to the void: looking to connect with fellow neuroscientists, interested in all things #stress, #locuscoeruleus #neuropeptides #ephys Particularly invested in dialogue, open science & equity
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Above, my #introduction of interests. Here, who I am, what I do: a neuroscientist at the #MRCLMB and University of Cambridge, UK, studying the neural circuit basis of behavior, originally in #Drosophila but now also in #cephalopods (#pygmysquid #Idiosepius), the lancelet #Amphioxus and other animals. Our main approach: whole brain #connectomics with #vEM (volume electron microscopy) as the basis for computational modeling to guide neuronal activity perturbation and monitoring experiments with #optogenetics and #electrophysiology (#ephys for short).
Once upon a time I founded the #ImageJ -based #TrakEM2 software for image registration and neuronal arbor reconstruction and annotation, which spurred founding the #FijiSc (https://fiji.sc) image processing software, and later the #CATMAID web-based software for #connectomics.
Always open to inquires from prospective students and postdocs, and collaborations. -
Next, https://onlinelibrary.wiley.com/doi/abs/10.1111/ejn.15866
Here authors go deep into slice #ephys to show cholinergic neuromodulation of #LC NAergic cells and periLC #interneurons, via muscarinic Ach receptors.
In an interesting twist, mAchR activation *both* increases spontaneous activity of the forementioned cell types, *and* suppresses inhibitory input to LC-NA neurons.
Data indicate that, in a receptor-specific manner, cholinergic neuromodulation alters E/I relations within the LC
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#introduction toot!! I am a neuroscientist at Instituto Cajal in Madrid, Spain. My lab studies how the 🧠hippocampus generates activity patterns (theta, gamma and ripple oscillations) in service for memory function. We target cell-type specific microcircuits and basic neurophysiological mechs in health & disease (e.g., epilepsy). We use #ephys #neuropixels #miniscopes #uLEDs #optogenetics #computationalneuroscience #machinelearning and love developing new #openscience tools & #neurotechnologies
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#ephys study of monkeys reveals a 2-stage mechanism for recalling #SemanticMemory: 1. retrieve its allocentric representation in #PerirhinalCortex, 2. represent the retrieved information in the 1st-person perspective by #hippocampal neurons #PLOSBiology https://plos.io/3qB4Olx
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#NeuroMastodon #ephys #spikesorting
SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/
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:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.htmlHappy #spikesorting to everyone!!!
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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/spiketutorialsCheck out the source code:
https://github.com/SpikeInterface/spikeinterface/Happy #spikesorting to all!
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@kordinglab @PessoaBrain oh boy I've got to read both pieces because I don't know how one would argue about the existence and importance of switching networks. They also don't seem at all at odds with modular networks.
Work from the extended Eve Marder universe on the Crab #STG, #Neuromodulation, and #ContextualModulation as always is useful here: In a network of just 40-ish neurons, there are clear sub circuits with clearly defined computations with cells with well defined roles. There are also neurons that belong to multiple circuits, linking them together and qualitatively changing both their and the jointly-defined circuits behavior per neuromodulation, longer timescale circuit rhythms, and behavioral/organismal context. It seems extremely unlikely to me that this is a byproduct of the particular ganglion, by far the more parsimonious interpretation is that this is fundamental to how densely connected excitable dynamical systems with diverse functional requirements work - the combinatoric computational benefits are obvious, and the empirical fact of their existence is impossible to deny.
Haven't read the piece(s) yet and would be surprised if they didn't mention this work. Can pull citations and more detailed argument when at computer. it hardly makes me an expert but Lauren Hewitt and I did a project on this at the #MBL with some #DynanicClamp #EPhys , so I already have the argument organized.
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#Neuroscience #Ephys 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 #Tetrodes.
The x-axis scale for each of the two columns is 1s.
#Electrophysiology -
@elduvelle We are a #neuroscience lab and I consider myself a #neuroscientist. We do both #Ephys and #CalciumImaging in the lab, but I don't do it myself personally–I wish. At least I do some of the software programming, which I enjoy immensely.
