Best time and place to realize that you don’t have access to your animal unit past midnight is definitely not at 12:05 AM, in front of the animal unit, with a rat 🙃 #PostDocLife
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?
@jonny thank you! It’s great that you have some doc for it! I’ll be helping set up a new lab soon and this might come in handy - I’ll probably ask you more about this in a few months.
My current lab already has a NAS I think but at the moment I’m looking for a backup for that as none of my computers have enough storage to hold all the data at once and I don’t really like having it just in one place, even if that’s on a RAID system
@jonny supposedly, as shown in this #BuszakiLab paper ⬇️ but I wonder if there is something a bit more clear-cut…
Generally when I see a symmetrical (mexican hat) waveform I consider it’s an axon / fiber, and large interneuron or pyramidal waveforms are clearly from the cell body but it’s all quite handwavy…
The last #HyperDriveI’ll be building here in the US!
(I’m leaving my current postdoc in 6 weeks to go on holidays and then maybe another postdoc in Glasgow!) #PostDocLife
as long as I have the attenion of the HPC folks-- what are we doing these days when bootstrapping for place cell mutual info? shuffling positions and keeping spike times (and thus ISI) constant, or shuffling spike times? Seen both in papers and unsure if there is a consensus
@aheadofthenerve I would say shuffle the spike trains (so not randomly shuffle the times of spikes but shift them all of the same amount for each shuffle to maintain firing statistics but disrupt the relation of the firing with location). Also I would make sure to use high within-session stability as an additional criterion for place cells. Looking forward to a sneak peek of your data :)
@aheadofthenerve I don’t recall seeing position shuffling or even shifting for characterization of place cells but maybe that’s for calcium imaging when you don’t have access to spike? I would say the standard is what I said above for ephys data. Shuffling position seems bad. Shifting position seems like it should be exactly the same as shifting times no?
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?
@jonny@chrisXrodgers haha indeed he’s been helping with that same question on the NeuroMethods slack!
I have to say, now that I’ve tried the single-tetrode with small (12.7 microns) nichrome wire, using precise shuttles (metal, not 3D printed), the movements are surprisingly responsive! Sure, the brain is jello, but these tetrodes are quite stiff, so they seem to move well (as far as I can see from looking at and listening to the signals, at least).
@jonny@aheadofthenerve it took me a while to find the best sleep box but I ended up using an empty cage with some cloth towels and paper towels.. worked pretty well, and easy to clean!
This was an earlier prototype:
There used to be tools for that but I don’t know it they still work, I’m sure others will have more insights.
To find Neuro people, you can look at the accounts I follow with this account, or check out the #Neuroscience or #Neuroscientist hashtag.
Also, the best thing is usually to write an # Introduction post (with the actual hashtag) telling people a bit about you and your interests and what you plan to post about - then check out who’s boosting it or following you and you can follow them if you want.
Let us know if you have any questions! And Welcome! 🤗
@aheadofthenerve Hope you’ll bring all your still-on-twitter friends on here!
Also, our instance (neuromatch.social) and many others have defederated from Threads (for many reasons, among which their transphobic content which is against our rules). If they fix it we might eventually connect back…
@jonny Yes! But someone improved the formatting, it looks much cleaner now than when I wrote it 😅
You’re right, I could add a “special neuroscientists” paragraph!
#Consciousness question from someone who read #philosophy stuff on this years ago but nothing from #neuroscience. Is it generally understood to be a memory phenomenon? It seems logically that it must be (see below), but that's not the way the philosophy stuff I have read about it discussed it.
My argument is that the only thing we could be talking about if we're talking consciousness is things that have made their way into a specific memory subsystem (the ones that are accessible to our language systems), otherwise we wouldn't be able to talk about it. Similarly, anything that has made its way into that memory subsystem would also be something we were conscious of. In other words, consciousness is just the set of things that go into that subsystem.
So is consciousness just the study of some particular memory subsystem and the way it interacts with other systems like language? And if we don't understand how memory works, can we understand anything about consciousness?
@neuralreckoning not an expert but isn’t consciousness also about immediate sensations and not just memorized events? Like, I get hurt by something, I am then conscious of the pain, or even if I’m staying immobile doing nothing and trying to think of nothing.. I am conscious of breathing and sitting on the couch?
For me consciousness is just the neural activations happening in your brain that are coherent enough that they pass a threshold for you to be aware of it. Sensation, memory, action, could be anything…
Periodic reminder of what fMRI's BOLD signal is measuring, and its temporal dynamics:
"blood oxygenation level–dependent (BOLD) contrast. [...] increased signal in a voxel measured with an EPI [echo planar imaging] sequence indicates recent neuronal activity because of the relative increase in local blood oxygenation that accompanies such activity. The temporal profile of this BOLD response, known as the hemodynamic response function, looks like a bell curve with a long tail, peaking around 4 to 5 seconds after local neural activity and returning to baseline after 12 to 15 seconds."
From "Principles of Neural Science", Kandel et al. 6th edition, page 115.
No matter how fast the EPI imaging is (~100 ms), the BOLD dynamics makes GCaMP look lighting fast. Temporally deconvolving BOLD is possible, to a point, but remember its spatial resolution is measured in millimetres, whereas neuronal somas measure ~0.025 millimetres.