Julie Fabre

We're looking for a research assistant to work in our neuroscience lab at @princetonneuro.bsky.social @hhmi.org where we study learning and decision-making circuitry.

Apply here: research-princeton.icims.com/jobs/21001/r...

Pls share w/ anyone who might be interested!

New by Agnès Landemard (@agnesland.bsky.social‬) & co

Brainwide blood volume reflects opposing neural populations

Brainwide fluctuations in blood volume arise from two populations with opposite relation to brain state and distinct relationships to blood supply

www.biorxiv.org/content/10.1...

Congrats!! 🎉

For now it is compatible with Kilosort only. However we want to extend this! The fastest way would be to create a github issue / email me so I can add support for another sorter. We're also keen to integrate / be compatible with the amazing spike interface - stay tuned for that :)

High-dimensional neuronal activity from low-dimensional latent dynamics: a solvable model Computation in recurrent networks of neurons has been hypothesized to occur at the level of low-dimensional latent dynamics, both in artificial systems and in the brain. This hypothesis seems at odds ...

The firing of neural populations is high-dim even if their subthreshold activity is low-dim! This work by @bio-emergent.bsky.social and @haydari.bsky.social shows how, with a solvable model, a data analysis technique, and data from mouse visual cortex: www.biorxiv.org/content/10.1...

Big thanks to Sam Dodgson and @maxime-beau.bsky.social for help with this Python version

🧠 BONUS: bombcell can also calculate ephys properties and classify your striatal cells into MSN/FSI/TAN (and UIN) categories!

📈 How well does it work?
Preliminary data shows bombcell correctly labels white matter units, agrees with manual curation, and it is already in use in an estimated 30+ labs

Users can now also manually label a subset of units in the GUI, and bombcell will automatically suggest the optimal parameter thresholds for your dataset.

📊 Key feature
An important part of bombcell is the ability to quickly look at your data and quality metrics, using summary plots and an interactive GUI. Visual feedback makes it simple to fine-tune parameters for your specific needs.

🔧 How does it work?
bombcell uses a comprehensive set of quality metrics (waveform shape, ISI violations, drift, amplitude, spatial spread, refractory period violations, etc.) with tunable thresholds to automatically classify your units as good, MUA, noise or non-somatic.

GitHub - Julie-Fabre/bombcell: Automated quality control, curation and neuron classification of spike-sorted electrophysiology data Automated quality control, curation and neuron classification of spike-sorted electrophysiology data - Julie-Fabre/bombcell

🚀 We are excited to share that bombcell is now available in Python! 🐍 Automatically sort your units into good/MUA/noise/non-somatic using quality metrics and interpretable & adjustable classification thresholds.
pip install and play around with our toy dataset:
🔗 github.com/Julie-Fabre/...

Our work, out at Cell, shows that the brain’s dopamine signals teach each individual a unique learning trajectory. Collaborative experiment-theory effort, led by Sam Liebana in the lab. The first experiment my lab started just shy of 6y ago & v excited to see it out: www.cell.com/cell/fulltex...

Dynamic basal ganglia output signals license and suppress forelimb movements - Nature Basal ganglia output neurons fire dynamically in bidirectional and movement-specific patterns to license forelimb movements. 

Forelimb movement control at the basal ganglia - brainstem interface!

Happy to finally share this work from me and @harsh-kanodia.bsky.social with Silvia Arber!

@biozentrum.unibas.ch @fmiscience.bsky.social

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

Bombcell icon

🔊New resource: Bombcell, automated quality control for extracellular electrophysiology
💡This is an #opensource, user-friendly toolbox that streamlines quality control for spike sorting outputs.
👩‍🔬Develop by Julie M. J. Fabre
🔗Link: open-neuroscience.com/en/post/bomb...
#OpenScience #Neuroscience

we're crowd-sourcing a searchable repository of tangible benefits stemming from federally-funded research. Come enjoy the great stories; or send in an idea; or volunteer to join the team.

publicusaresearchbenefits.com

please share and re-share so we get more great stories in there!

Many of us use 2p scopes to image 3D volumes of brain. But then we analyze the data plane by plane, resulting in duplicated neurons, missed neurons, and low s/n. Let's go 3D!

Suite3D: Volumetric cell detection for two-photon microscopy
by @haydari.bsky.social & team.
www.biorxiv.org/content/10.1...

🎓 Qu’est-ce que le programme Médecine-Sciences ? Après dix ans d'existence, quel bilan ? Son directeur, Alain Bessis, professeur attaché à l'ENS-PSL et directeur de recherche au CNRS revient sur la décennie écoulée et les enjeux pédagogiques du programme. 

À lire ici 👉 bit.ly/3Gm0RsA

Two neurons in front of a Neuropixels probe. One neuron says to the other: "Don't look, but I think we're being followed!".

Our paper describing UnitMatch software "tracking neurons across days with high-density probes", appeared in this month's issue of #NatureMethods. Missed it? Read it here: www.nature.com/articles/s41...

A neural mechanism for learning from delayed postingestive feedback - Nature Illness signals from the gut reactivate and strengthen flavour representations in the amygdala to support learning from delayed postingestive feedback.

How do we associate the flavors we experience during a meal 🍽️😋 with postingestive effects like food poisoning 🤢🤮 that arise much later?

Our answer in @nature.com this week: Illness signals from the gut reactivate and strengthen flavor representations in the amygdala.

📄: nature.com/articles/s41...

UCL early career researchers selected as 2025 Schmidt Science Fellows Two UCL researchers have been named as Schmidt Science Fellows, an award only given to 32 exceptional early career researchers worldwide.

Two UCL researchers, including Dr Julie Fabre (@uclqsion.bsky.social) have been named as Schmidt Science Fellows, an award given to 32 exceptional early career researchers worldwide.
Congratulations to both Dr @juliefabre.bsky.social & Dr Almarri on this incredible achievement! 👏

Thank you, Laura!!

GitHub - Julie-Fabre/bombcell: Automated quality control, curation and neuron classification of spike-sorted electrophysiology data Automated quality control, curation and neuron classification of spike-sorted electrophysiology data - Julie-Fabre/bombcell

First off, Bombcell is a MATLAB package (python version coming) developed by @juliefabre.bsky.social. It uses several metrics, like waveform shape, spike amplitudes and drift, to determine whether a detected unit is noise, multi-unit activity, axonal or a single neuron.
github.com/Julie-Fabre/...

Personally I 💙 bombcell (: works really well in removing non-somatic and noisy units. As for MUA vs single it’s a bit trickier and probably based on how many RPV one can accept but still does a good enough job

This is awesome!!

I am very proud to announce that my PhD paper finally came out in Cell! In this *very* collaborative study, we develop and release a deep-learning approach to predict neuron type identity from their electrical signature. doi.org/10.1016/j.ce... 1/16 🧵