Guido Meijer

The Power Pixels ⚡ pipeline is out now in Peer Community Journal!

Are you doing Neuropixel recordings but don't have a pre-processing pipeline yet? Check out this end-to-end pipeline designed to simplify preprocessing of Neuropixel recordings 🧠

peercommunityjournal.org/articles/10....

A prefrontal cortex map based on single-neuron activity - Nature Neuroscience The authors mapped spontaneous and choice activity across mouse prefrontal cortex. The activity maps aligned with intrinsic connectivity rather than anatomical subregions, suggesting that connectivity...

Main postdoc study out! We can redefine prefrontal cortex regions with single-unit activity! Grateful to @carlenlab.bsky.social and @weltgeischt.bsky.social who made this crazy project real. Thanks to all co-authors, collaborators, and reviewers.
www.nature.com/articles/s41...

BOLD signal changes can oppose oxygen metabolism across the human cortex, Nature Neuroscience

fMRI signals “up,” but neural metabolism might be going “down.”

In our @natneuro.nature.com paper, we demonstrate that about 40% of voxels with robust BOLD responses exhibit opposite oxygen metabolism, revealing two distinct hemodynamic modes.

rdcu.be/eUPO8
funds @erc.europa.eu
#neuroskyence 🧵:

The Power Pixels pipeline just keeps getting better! The latest update comes with:
- OpenEphys support
- AP_Histology support
- automatic high-frequency noise reduction
- NWB format export option
- zarr compression of raw data

And, most importantly: a cool new logo!

github.com/NeuroNetMem/...

Halloween isn’t my thing. My idea of a scary night is reading the plots of horror movies on Wikipedia.

I never understood why everyone always complains about the clocks changing.
Then I had a kid.

Thanks! I always save the illustrator file as an editable pdf, that way it is self contained even when the panels are technically links.

Thanks! Yes, that's a good way of doing it if you don't like Illustrator, I just find it way too time consuming to position everything programmatically (and I have free Adobe through my uni 😁)

I didn't know that, that's cool!

Google Colab

I hope you found this useful! Here is a Google Colab with example code of what was discussed in this thread:

colab.research.google.com/drive/1UlCET...

The workflow: Python plots single panels, saved as pdfs. Create an empty figure of 7 inch (180 mm) wide in Illustrator and place the panels as links. Add the panel letters (a,b,c). Now, if a new version of a panel is generated you just have to click update links in Illustrator and it's there. 🤩

A note about colors 🌈 Imagine you made eight figures and your PI asks you to change the color of an element you've consistently plotted green into orange. If you define your colors in the plotting function you only have to change it there and rerun the plotting scripts, this save a lot of time!

Full width figures typically have four panels next to each other, a good rule of thumb is that a single panel is 1.75 by 1.75 inch. Create two figure panels like this:

f, axs = plt.subplots(1, 2, figsize=(1.75 * 2, 1.75), dpi=300)

⚠️ If it's too small increase the dpi, not the figsize!

The font size of each plot element can be easily set with seaborn. Write a function like this that sets the font size and any other style element you like to have in all your plots and the function each time before plotting (link to the code in the last post).

Journals have criteria figures have to adhere to. Generally, a full-width figure should be 7 inch wide and font sizes cannot be smaller than 7 pts. If you get into the habit of always creating figures that fit these criteria this will save you a lot of time when submitting.

Want to make publication-ready figures come straight from Python without having to do any manual editing? Are you fed up with axes labels being unreadable during your presentations? Follow this short tutorial including code examples! 👇🧵

I was doing the second-to-last recording of my project and was happily thinking to myself that I haven't broken a single Neuropixel in the entire two year project.

You can guess what happened next...

Now I have to install a new probe just for one final recording 🙃

I love how they came up with all this random stuff but for this one area they were like "I really don't know, just put a question mark"

Getting a hundred bucks would have been nice! We had to pay them twelve thousand bucks instead.

When I told my dad I published in Nature he was like "wow, you must have made a lot of money with that"

Of course, that makes complete sense 🙃

I don't know why people say X is going down the drain, my last post got lovely replies like this one:

Want to collaborate with the International Brain Laboratory on your own project? We have funding to work with groups anywhere in the world to do new large-scale projects and we are looking for new partners! Learn more and apply: www.internationalbrainlab.com/ibl-core-apply

Thrilled to share that our work is now published in Science! ✨

We found a preference for visual objects in the mouse spatial navigation system where they dynamically refine head-direction coding. In short, objects boost our inner compass! 🧭

www.science.org/doi/10.1126/...

🧵1/

If you're into podcasts, here's a good one on the @intlbrainlab.bsky.social brainwide map, by @newscientist.com

www.newscientist.com/podcasts/fir...

A brain-wide map of neural activity during complex behaviour - Nature The International Brain Laboratory presents a brain-wide electrophysiological map obtained from pooling data from 12 laboratories that performed the same standardized perceptual decision-making task i...

Sad day for peope who still believe brain areas are the primary organizational units of function in the brain.

www.nature.com/articles/s41...

How Do Our Brains Make Decisions? The International Brain Laboratory Is Closing In on Answers How Do Our Brains Make Decisions? The International Brain Laboratory Is Closing In on Answers on Simons Foundation

The ‪@intlbrainlab.bsky.social published 2 papers today on their work to create a map of neural activity across the entire mouse brain. Learn more about the lab: https://www.simonsfoundation.org/2025/02/20/how-do-our-brains-make-decisions-the-international-brain-laboratory-is-closing-in-on-answers/

First map of mammal brain activity may have shown intuition in action Scientists have mapped the activity that takes place across a mouse's entire brain as it decides how to complete a task - and the results could explain the origin of our gut feelings

The first complete activity map of a mammalian brain has revealed unprecedented insights into how decisions are made – and may even hint at the roots of intuition.

Extremely proud to have contributed to this monumental effort of recording the entire mouse brain, at cellular resolution, during complex behavior 🧠🐭

Artificial dural sealant that allows multiple penetrations of implantable brain probes This study reports extensive characterization of the silicone gel (3-4680, Dow Corning, Midland, MI), for potential use as an artificial dural sealant…

PSA: don't buy duragel from Cambridge Neurotech, it's a scam! 🚨

They charge $200 (incl. shipping) for a 16 ml spout. But duragel is just DOWSIL 3-4680 (see paper below) of which you can buy a large container of 210 ml for only $110. That's 24 times cheaper! 💸

www.sciencedirect.com/science/arti...