#tetrodes — Public Fediverse posts

#NeuroMethods question:
What do you all (experimentalists or computational people) prefer as a format to store and share #Electrophysiology data? Either for Tetrodes or Probes? And why? 👀

Is NWB (Neuroscience Without Borders) the gold standard?

#Neuroscience #Tetrodes #Probes #DataManagement

#NeuroMethods question:
What do you all (experimentalists or computational people) prefer as a format to store and share #Electrophysiology data? Either for Tetrodes or Probes? And why? 👀

Is NWB (Neuroscience Without Borders) the gold standard?

#Neuroscience #Tetrodes #Probes #DataManagement

@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.

@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.

Ok maybe this is the best cluster space ever
(also, from an implant that’s almost 4 months old!)
#Tetrodes #NeuroRat #Hippocampus #PlaceCells

Ok maybe this is the best cluster space ever
(also, from an implant that’s almost 4 months old!)
#Tetrodes #NeuroRat #Hippocampus #PlaceCells

I bet you’ve never seen a bigger… cluster than my one 😁
(Well, technically, my #NeuroRat’s)
#Hippocampus #Tetrodes

I bet you’ve never seen a bigger… cluster than my one 😁
(Well, technically, my #NeuroRat’s)
#Hippocampus #Tetrodes

@BlakeP_Neuro I think I got the same as you, but in #Hippocampus!!
#Tetrodes #NeuroRat

@BlakeP_Neuro I think I got the same as you, but in #Hippocampus!!
#Tetrodes #NeuroRat

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

#NeuroMethods question:

What is the smallest optimal distance between independent #Tetrodes in dorsal CA1 (so that you don’t record from the same neuron in adjacent tetrodes and also movement of one doesn’t influence the movement of others)?
Say, using 12.7 μm diameter wire?

#Neuroscience #Hippocampus #Electrophysiology

#NeuroMethods question:

What is the smallest optimal distance between independent #Tetrodes in dorsal CA1 (so that you don’t record from the same neuron in adjacent tetrodes and also movement of one doesn’t influence the movement of others)?
Say, using 12.7 μm diameter wire?

#Neuroscience #Hippocampus #Electrophysiology

It’s tetrode-making season!
#Tetrodes

Do I know anyone using the #NeuroMouse version of the #ShuttleDrive?
(Small, 32 (or 16?) tetrodes version)

If so can you tell me what you think in terms of stability, recording quality etc?
https://open-ephys.org/shuttledrive

Edit: still looking for labs using this in 2025!

#OpenEphys #HyperDrive #Tetrodes #NeuroMethods

*** Hyperdrive Spreadsheet for #Electrophysiologists reminder ***

It’s a collaborative online spreadsheet that you can just check out or even contribute to!

Goals:
-> check how other scientists build & implant drives for tetrode & probe freely-moving electrophysiology

-> try to link building / surgery parameters to specific problems

-> open to all: add a new row for each drive type that you’ve used!

Any questions: ask them as comments in the spreadsheet!

https://docs.google.com/spreadsheets/d/1_RQzEL3dPUSTLOz9AyFzJbuIaXmG7jZLt3z06Fllemc/edit?usp=sharing

#NeuroMethods #Neuroscience #Tetrodes #Electrophysiology

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

@elduvelle_neuro as someone who used #Tetrodes for quite a few years in both #rats and #mice, i'd strongly urge people to use high-density #probes if possible! far more cost effective, more data, less animals, less time. tetrodes should be the exception when recording geometry or other issues demand it.

@elduvelle_neuro as someone who used #Tetrodes for quite a few years in both #rats and #mice, i'd strongly urge people to use high-density #probes if possible! far more cost effective, more data, less animals, less time. tetrodes should be the exception when recording geometry or other issues demand it.

@danbirman Since you asked… can you make a #Screening software (/robot) that will use LFP and spiking characteristics to tell you if and how much to lower your #tetrodes of? 🙂
(I actually enjoy screening.. but it can take a long time)

@danbirman Since you asked… can you make a #Screening software (/robot) that will use LFP and spiking characteristics to tell you if and how much to lower your #tetrodes of? 🙂
(I actually enjoy screening.. but it can take a long time)

Hmm maybe this one is better… not sure 🤔 😁
#Tetrode #Tetrodes #Hippocampus #Screening

Hmm maybe this one is better… not sure 🤔 😁
#Tetrode #Tetrodes #Hippocampus #Screening

#Hippocampus #Ripples - aren’t they the best? (with sound)
Notice how most of them show a positive deflection (positive Sharp-Wave) while the tetrode at the bottom right shows a negative SW, because it’s been moved past the CA1 cell layer!
(Data shown is from 16 #Tetrodes aimed at dorsal CA1, arranged in moveable bundles indicated by the colour)
#NeuroRat #Neuroscience

#Hippocampus #Ripples - aren’t they the best? (with sound)
Notice how most of them show a positive deflection (positive Sharp-Wave) while the tetrode at the bottom right shows a negative SW, because it’s been moved past the CA1 cell layer!
(Data shown is from 16 #Tetrodes aimed at dorsal CA1, arranged in moveable bundles indicated by the colour)
#NeuroRat #Neuroscience

#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

#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

What tags are you all following?
Here are mine but I’d like to add some more, particularly science-related:

#FediTips #Hippocampus #PlaceCells #Tetrodes #NatureIsBeautiful (yes… I’m the only one using it for now) #NeuroPaper #NeuroPaperThread #Neuroscience

What tags are you all following?
Here are mine but I’d like to add some more, particularly science-related:

#FediTips #Hippocampus #PlaceCells #Tetrodes #NatureIsBeautiful (yes… I’m the only one using it for now) #NeuroPaper #NeuroPaperThread #Neuroscience

Spike-sorting, before /after

This uses the automated method Klustakwick and then some manual refinement

#PlaceCells #SpikeSorting #Tetrodes #Neuroscience

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 *

#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 *

⤵️​ We have signals! I think… I’ve never implanted that high in cortex. It’s definitely very silent for now. Does it look normal to you?
The timescale is 2s; this shows the unfiltered and unreferenced signals. There are a few disconnected channels.

After trying it out, I still don’t understand the point of implanting your #Tetrodes out of the brain and wait until the end of the surgery to lower them. I much prefer watching them go in the brain, so I know what’s happening! And it’s also much faster.

⤵️​ We have signals! I think… I’ve never implanted that high in cortex. It’s definitely very silent for now. Does it look normal to you?
The timescale is 2s; this shows the unfiltered and unreferenced signals. There are a few disconnected channels.

After trying it out, I still don’t understand the point of implanting your #Tetrodes out of the brain and wait until the end of the surgery to lower them. I much prefer watching them go in the brain, so I know what’s happening! And it’s also much faster.

⤵️​ Giving the final touches to the #HybridDrive

In more details:

1. Adding the cone
   (painted with conductive epoxy, connected to the drive’s ground, to (try and) shield it from electrical interference, but it’s the first time I do this so I don’t know if it will work. Once on the rat, it will have a cap as well, except when plugged into the recording system.)

2. #GoldPlating
   This drive has 2 sets of tetrodes: 13 microns Nichrome wire and 17 microns Platinum-Iridium wire (testing which is best). Due to different wire material and diameter, they get gold-plated slightly differently; see this for a good plating tutorial for 12-13 um Nichrome, generously shared by John Bladon: https://github.com/elduvelle/ephys_tutorials/blob/main/4_gold_plating_Nichrome_12um.md

3. View of the finished drive.
   I am also testing the effects of implanting the tetrodes directly in the brain during surgery, or keeping them retracted in the drive and only lower them at the end of the surgery. This is for a bilateral dorsal #Hippocampus implant so it has two groups of tetrodes. I personally do not understand the point of not implanting directly in brain…

4. The guide/outer cannulas and their #Tetrodes
   Each guide cannula holds 4 tetrodes which move together, excepted 1 cannula that holds a single tetrode - to be left in the corpus callosum and used for reference. If everything works as planned. I used 27 gauge (thin walled) inner cannulas to guide the tetrodes - the smaller diameter that you can see); these do not move, only the shuttles and the tetrodes move.

Next step is implantation surgery!

⤵️​ Giving the final touches to the #HybridDrive

In more details:

1. Adding the cone
   (painted with conductive epoxy, connected to the drive’s ground, to (try and) shield it from electrical interference, but it’s the first time I do this so I don’t know if it will work. Once on the rat, it will have a cap as well, except when plugged into the recording system.)

2. #GoldPlating
   This drive has 2 sets of tetrodes: 13 microns Nichrome wire and 17 microns Platinum-Iridium wire (testing which is best). Due to different wire material and diameter, they get gold-plated slightly differently; see this for a good plating tutorial for 12-13 um Nichrome, generously shared by John Bladon: https://github.com/elduvelle/ephys_tutorials/blob/main/4_gold_plating_Nichrome_12um.md

3. View of the finished drive.
   I am also testing the effects of implanting the tetrodes directly in the brain during surgery, or keeping them retracted in the drive and only lower them at the end of the surgery. This is for a bilateral dorsal #Hippocampus implant so it has two groups of tetrodes. I personally do not understand the point of not implanting directly in brain…

4. The guide/outer cannulas and their #Tetrodes
   Each guide cannula holds 4 tetrodes which move together, excepted 1 cannula that holds a single tetrode - to be left in the corpus callosum and used for reference. If everything works as planned. I used 27 gauge (thin walled) inner cannulas to guide the tetrodes - the smaller diameter that you can see); these do not move, only the shuttles and the tetrodes move.

Next step is implantation surgery!

@chrisXrodgers Yes - that's the idea! But not everyone likes them, some prefer non-serrated scissors. At the moment I use serrated for bundles between 1-4 tetrodes and flat for larger bundles. Here's an example of a bundle of 8 #Tetrodes :

@chrisXrodgers Yes - that's the idea! But not everyone likes them, some prefer non-serrated scissors. At the moment I use serrated for bundles between 1-4 tetrodes and flat for larger bundles. Here's an example of a bundle of 8 #Tetrodes :

⤵️​ my favourite view: nicely cut #Tetrodes! (Diameter may be 13 or 17 microns)

⤵️​ my favourite view: nicely cut #Tetrodes! (Diameter may be 13 or 17 microns)

Here’s what I’m working on at the moment: a 32 #Tetrodes “hyperdrive” for bilateral hippocampal recordings. It’s a prototype - I’ll let you know if it works...🤞​

Here’s what I’m working on at the moment: a 32 #Tetrodes “hyperdrive” for bilateral hippocampal recordings. It’s a prototype - I’ll let you know if it works...🤞​

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/

@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

@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