#neuromethods — Public Fediverse posts

Slightly technical coding question, #Matlab to #Python:
What's the simplest way to read a Matlab table in Python?
Or, if that's not possible, what should I convert my Matlab table to so I can read it in python? 🙏
It's quite a big table with "nested" data i.e. some of the columns contain different-lengths arrays for each row and some contain matrices.

Links I've tried without success:
https://stackoverflow.com/questions/25853840/load-matlab-tables-in-python-using-scipy-io-loadmat (csv doesn't save all the data)
https://pythonguides.com/python-scipy-load-mat-file/ (about reading .mat files but does not seem to work with tables)

Links I haven't tried:
https://www.mathworks.com/help/matlab/matlab_external/use-matlab-tables-and-timetables-in-python.html (I believe this relies on having a working version of Matlab to use Matlab.engine to read the file, which kinds of defeats the purpose)

#Programming #NeuroMethods

Slightly technical coding question, #Matlab to #Python:
What's the simplest way to read a Matlab table in Python?
Or, if that's not possible, what should I convert my Matlab table to so I can read it in python? 🙏
It's quite a big table with "nested" data i.e. some of the columns contain different-lengths arrays for each row and some contain matrices.

Links I've tried without success:
https://stackoverflow.com/questions/25853840/load-matlab-tables-in-python-using-scipy-io-loadmat (csv doesn't save all the data)
https://pythonguides.com/python-scipy-load-mat-file/ (about reading .mat files but does not seem to work with tables)

Links I haven't tried:
https://www.mathworks.com/help/matlab/matlab_external/use-matlab-tables-and-timetables-in-python.html (I believe this relies on having a working version of Matlab to use Matlab.engine to read the file, which kinds of defeats the purpose)

#Programming #NeuroMethods

Slightly technical coding question, #Matlab to #Python:
What's the simplest way to read a Matlab table in Python?
Or, if that's not possible, what should I convert my Matlab table to so I can read it in python? 🙏
It's quite a big table with "nested" data i.e. some of the columns contain different-lengths arrays for each row and some contain matrices.

Links I've tried without success:
https://stackoverflow.com/questions/25853840/load-matlab-tables-in-python-using-scipy-io-loadmat (csv doesn't save all the data)
https://pythonguides.com/python-scipy-load-mat-file/ (about reading .mat files but does not seem to work with tables)

Links I haven't tried:
https://www.mathworks.com/help/matlab/matlab_external/use-matlab-tables-and-timetables-in-python.html (I believe this relies on having a working version of Matlab to use Matlab.engine to read the file, which kinds of defeats the purpose)

#Programming #NeuroMethods

Slightly technical coding question, #Matlab to #Python:
What's the simplest way to read a Matlab table in Python?
Or, if that's not possible, what should I convert my Matlab table to so I can read it in python? 🙏
It's quite a big table with "nested" data i.e. some of the columns contain different-lengths arrays for each row and some contain matrices.

Links I've tried without success:
https://stackoverflow.com/questions/25853840/load-matlab-tables-in-python-using-scipy-io-loadmat (csv doesn't save all the data)
https://pythonguides.com/python-scipy-load-mat-file/ (about reading .mat files but does not seem to work with tables)

Links I haven't tried:
https://www.mathworks.com/help/matlab/matlab_external/use-matlab-tables-and-timetables-in-python.html (I believe this relies on having a working version of Matlab to use Matlab.engine to read the file, which kinds of defeats the purpose)

#Programming #NeuroMethods

Slightly technical coding question, #Matlab to #Python:
What's the simplest way to read a Matlab table in Python?
Or, if that's not possible, what should I convert my Matlab table to so I can read it in python? 🙏
It's quite a big table with "nested" data i.e. some of the columns contain different-lengths arrays for each row and some contain matrices.

Links I've tried without success:
https://stackoverflow.com/questions/25853840/load-matlab-tables-in-python-using-scipy-io-loadmat (csv doesn't save all the data)
https://pythonguides.com/python-scipy-load-mat-file/ (about reading .mat files but does not seem to work with tables)

Links I haven't tried:
https://www.mathworks.com/help/matlab/matlab_external/use-matlab-tables-and-timetables-in-python.html (I believe this relies on having a working version of Matlab to use Matlab.engine to read the file, which kinds of defeats the purpose)

#Programming #NeuroMethods

RE: https://fosstodon.org/@zulip/115612910439118165

Just realised that #Zulip (a #Slack equivalent) is on Mastodon!

Have you tried it, if so do you like it? I'm thinking that #NeuroMethods could maybe move there (at some point in future)...

#AcademicChatter

Following-up on this, I have asked the following question on #NeuroMethods without success:

Anyone knows of any (published or not, successful or not) replication attempts of the #Tolman Sunburst maze "shortcut" task, in mice?

I'm also interested in info on any kind of unpublished replication attempt, in any species...

#Neuroscience #NeuroMice #Shortcut #CognitiveMap

#NeuroMethods I am looking for a UK supplier of thin metal cannulas.
Specifically, I would like a relatively small one (27Ga, thin wall, this one: https://componentsupplycompany.com/hypodermic-tubing/304ss-thin-wall/htx-27t-30/

• but that is from a US company)

This one was recommended to me
https://www.coopersneedleworks.com/
but they cannot make 27 Ga :(

Any other suggestions? 🙏
#HyperDrive building

#NeuroMethods question for those doing rodent surgeries:
Has anyone tried out this Stoelting #Stereotax ? What did you think?

https://stoeltingco.com/Neuroscience/Digital-Rat-Stereotaxic-Instrument~9637

#NeuroSurgery

I've said it before but the #NeuroMethods slack is really useful for all #Neuroscience methods questions. Feel free to join at https://neuromethods.slack.com/ with your institutional email, or DM me if you can't join that way!

Hi all, the recurrent question of backing up (or not) #NeuroMethods slack is there again.
Lots of people are suggesting backing up the contents onto some #Google product, whether gmail or google docs. I know that gmail is not private (google analyses the contents of the mails) but is Google document private?
Otherwise is there an alternative to google docs that would actually be private? I imagine if it is private then it will not be free..

(Neuromethods is a discussion platform for when you have a problem or question about a #Neuroscience technique. It's on the free #Slack version so the history past 90 days is lost. See the previous time I have asked about this: https://neuromatch.social/@elduvelle/112766589207831557)

#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

#VTE detection: what's the best algorithm out there to detect Rat VTEs from 2D head position data (no HD data)?
By "best" I mean least effortful for the user...

I know that @adredish has the D-phil method (explained in Interactions between deliberation and delay-discounting in rats #RedishLab which is used quite a lot.

But also just found out about a different method from @jessetm explained in A Machine Learning Approach for Detecting Vicarious Trial and Error Behaviors #MizumoriLab - Jesse, I haven't checked the details yet but as its creator, would you recommend it? Would you have code for it somewhere? I couldn't see a repo link in the paper but maybe I missed it. 🙏

Edit: Jeff Stott added this one to the list, which uses a "Curvature" measure (also from #RedishLab): A functional difference in information processing between orbitofrontal cortex and ventral striatum during decision-making behaviour

Any other ones out there?
#Neuroscience #NeuroMethods #SpatialCognition

UK hardware question: where can you buy small metal cannulas, as well as polyimide and polymicro tubing? (Things used for #Hyperdrives)
I know the places for the US but have no idea for UK (where I am now)

Edit: by small I mean something in the range of 100-300 microns diameter

#NeuroMethods

@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.

#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 😬

Seen on the #NeuroMethods slack:

Any suggestions for algorithms to track pupil in mice? (Not #DeepLabCut )

#AnimalBehaviour #Tracking

The #NeuroMethods slack is an amazing resource for all #Neuroscience technical questions. However it’s using a free slack version so all older messages are hidden, and with new #Slack policies they’ll soon be deleted.

One solution would be to find one or several “sponsors” who would help move the slack to a paid version. Any ideas or suggestions about this?

(An older article on the Neuromethods slack: https://www.bna.org.uk/mediacentre/news/neuromethods-slack-group-a-new-platform-for-troubleshooting-methods-in-neuroscience/
The link to sign-in: https://neuromethods.slack.com/
Ask me here or in DM and I’ll invite you if you can’t sign in with your work email!)

@susanleemburg oh I saw your post on #NeuroMethods. Hope you find your answer!

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?

#Ephys #NeuroMethods #DataManagement

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

#NeuroMethods question:
Has anyone found a good, reliable, automatized way to deliver small liquid reward amounts for rodent experiments?

We’ve been using a pressurized air system with solenoid valves (from McMaster) but they are not very reliable and the quantity delivered fluctuates with time and depends on the actual valve…

We were thinking of testing out the Open Neuroscience / #LaubachLab syringe pump but someone just mentioned they are not that reliable for small volumes (1-10 microliters). Anyone else has feedback on them?

Anyone doing liquid reward delivery for rodent who has found the Valve Graal??
#Neuroscience #BehaviouralNeuroscience

What are some metals that rats not only cannot chew, but also do not like to chew on?
Trying to find the best material for a kind of nosepoke…
#NeuroMethods #NeuroRats

#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

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

@biogeo thanks for the details - very interesting!
The neurologger I know of is the #SpikeGadgets one and it records 128ch of high res LFP (unfiltered) so you can get spikes from that using any kind of filtering + spike detection. But it is not compatible with MRI. They also have one for Neuropixels probes but I haven’t tried it.

You might have more luck asking your question on the #NeuroMethods slack (https://neuromethods.slack.com/) - let me know if you need an invite!

@biogeo thanks for the details - very interesting!
The neurologger I know of is the #SpikeGadgets one and it records 128ch of high res LFP (unfiltered) so you can get spikes from that using any kind of filtering + spike detection. But it is not compatible with MRI. They also have one for Neuropixels probes but I haven’t tried it.

You might have more luck asking your question on the #NeuroMethods slack (https://neuromethods.slack.com/) - let me know if you need an invite!

@biogeo thanks for the details - very interesting!
The neurologger I know of is the #SpikeGadgets one and it records 128ch of high res LFP (unfiltered) so you can get spikes from that using any kind of filtering + spike detection. But it is not compatible with MRI. They also have one for Neuropixels probes but I haven’t tried it.

You might have more luck asking your question on the #NeuroMethods slack (https://neuromethods.slack.com/) - let me know if you need an invite!

@biogeo thanks for the details - very interesting!
The neurologger I know of is the #SpikeGadgets one and it records 128ch of high res LFP (unfiltered) so you can get spikes from that using any kind of filtering + spike detection. But it is not compatible with MRI. They also have one for Neuropixels probes but I haven’t tried it.

You might have more luck asking your question on the #NeuroMethods slack (https://neuromethods.slack.com/) - let me know if you need an invite!

@biogeo thanks for the details - very interesting!
The neurologger I know of is the #SpikeGadgets one and it records 128ch of high res LFP (unfiltered) so you can get spikes from that using any kind of filtering + spike detection. But it is not compatible with MRI. They also have one for Neuropixels probes but I haven’t tried it.

You might have more luck asking your question on the #NeuroMethods slack (https://neuromethods.slack.com/) - let me know if you need an invite!

I’ve started making tutorials for different #Tetrode #Electrophysiology steps here
The next ones are probably going to be Tetrode-making and drive-building.

Is there anything else that you’d like to see there?
#NeuroMethods

We often ask to what extent neural representations generalize across contexts - e.g., across time, experimental conditions, or between task variables. Using multivariate cross-decoding, we check whether a decoder, trained in one context, returns significant results in another context. In our new article (with Markus Siegel - and my first, and quite possibly last, in NeuroImage: https://www.sciencedirect.com/science/article/pii/S1053811923004093), we show that this approach is prone to false positives when applied to neural population data involving any signal mixing, such as M/EEG, fMRI, ECoG, LFP. #neuroscience #NeuroPapers #decoding #mvpa #eeg #meg #fmri #neurophysiology #electrophysiology #NeuroMethods @neuroscience @neurobuzz (1/7)

We often ask to what extent neural representations generalize across contexts - e.g., across time, experimental conditions, or between task variables. Using multivariate cross-decoding, we check whether a decoder, trained in one context, returns significant results in another context. In our new article (with Markus Siegel - and my first, and quite possibly last, in NeuroImage: https://www.sciencedirect.com/science/article/pii/S1053811923004093), we show that this approach is prone to false positives when applied to neural population data involving any signal mixing, such as M/EEG, fMRI, ECoG, LFP. #neuroscience #NeuroPapers #decoding #mvpa #eeg #meg #fmri #neurophysiology #electrophysiology #NeuroMethods @neuroscience @neurobuzz (1/7)

*** 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

The COMBO window: A chronic cranial implant for multiscale circuit interrogation in mice

”ChrOnic Multimodal imaging and Behavioral Observation”

”we demonstrate how the COMBO window facilitates the combination of optogenetics, fUS and electrophysiology in the same [head-fixed] animals”

#NeuroPreprint #NeuroMethods

@kevinbolding are you not on the #NeuroMethods slack? It can be very useful for this kind of questions!

https://neuromethods.slack.com/

Let me know if you’d like an invite link!

#NeuroMethods poll: which is your favourite manual #SpikeSorting (refinement) program?🧠🖥️

Polls don’t have enough options so detailed answers would be great 😃:

1: Klusters
2: Mclust
3: Offline Sorter
4: Phy
5: Spike Sort 3D
6: Tint (I didn't find a link describing the software)
7: Other
8: None (all automatised!)

(Note: I asked the same poll on the NeuroMethods SpikeSorting channel)

#Neuromethods question: what is the longest that you have seen rats stay immobile for a reward?
For me: ~6s but I wonder how much we can push it…

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)

@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!

#NeuroMethods #Histology question:
Have you ever skipped the cryoprotection step before freezing a brain (leaving it in 30% sucrose solution after it’s been left in formalin for a few days)?
If so did you notice any difference in the final appearance of the slides? Perhaps it depends on the way the brain is frozen?

(Mostly interested in those doing Cresyl Violet / Thionin staining but I’ll take anything)

thinking about making a set of dlx creOFF AAV constructs a la @JDimidschstein and @sohallab. before i do - has anyone got a stash? initially gfp / chr2 but also likely switch gfp/dtomato too. for some 'NOT x' experiments. would be nice if they already existed! #neuroscience #neuromethods #aav #mouse #interneurons HT @elduvelle for the hashtags!