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?
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
I think I may have DeadSalmonfMRI’d insect field-potentials. Was teaching ephys to some gradstudents and wanted to emphasize the importance for controlling for mechanical artifacts. So I showed them artifacts from dead animals and then for good measure - from an agarose gel.
All 3 rows show responses to gentle, unregulated airpuffs on a prep that was only electrodes placed on a piece of agarose.
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
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)
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!
I guess it's time to finelly do my #introduction !
I'm a PhD student in Michaël Zugaro's lab
I'm studying the interaction between spatial coding in the #hippocampus and reward representation by #dopamine signaling, especially the VTA - Nucleus Accumbens pathway.
Doing ephys extra-cellular recordings in freely mooving rats trying to catch some chocolate milk!
The dying bird convinced me that mastodon was the way to go and I'm glad to see the neuroscience community growing!
I'm a bit shy on social media but I'll boost everything related to the brain that I find interesting 🧠 #PlaceCell#neuroscience#reward
#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 #neuroscientsit. 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.
There is still time to apply for the iBio_Sorbonne #neuro#summerschool !! Come learn about computational #analysis for #behavior#ephys#imaging in the south of France #Banyuls Theory and hands-on training on real #datasets. It's cheap and travel help is available. Please spread widely!!
Is there any smart tool for extracting population spike times which would be more reliable than thresholding and removing synchrofacts and discard less data than single-unit extraction? #ephys
Very happy to announce that my lab "Physiology of Light perception" will open in January at the Dept of Ophthalmology of the Inselspital (@inselgruppe) in Bern, Switzerland 🇨🇭! 1/5 www.murelab.org
My lab will use #ephys, #-omics, and #circuittracing to bridge #retina and brain biology. I’ll post soon job ads but you can already send me an email if you're interested in a master/PhD/postdoc. Come work with me @unibe in beautiful Bern! 3/5 https://www.youtube.com/watch?v=Ahlse_WM0P8