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Julie Fabre

@juliefabre.bsky.social

160 followers 210 following 11 posts

Postdoc in Ilana Witten's lab. Former PhD student in Kenneth Harris and Matteo Carandini's lab. Follow for updates on bombcell and other Neuropixels software. https://github.com/Julie-Fabre

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Julie Fabre @juliefabre.bsky.social · Jun 13

🚀 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/...

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

github.com

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Reposted by Julie Fabre

Matteo Carandini @carandinilab.net · 9d

Neuropixels Ultra!

By @steinmetzneuro.bsky.social, who led a big collaboration

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

Ultra-high-density Neuropixels probes improve detection and identification in neuronal recordings

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single-neuron and single-spike re…

www.sciencedirect.com

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Reposted by Julie Fabre

Thomas Luo @thomas-zhihao-luo.bsky.social · 22d

How does the brain decide? 🧠

Our new @nature.com paper shows that neural activity switches from an 'evidence gathering' to a 'commitment' state at a precise moment we call nTc.

After nTc, new evidence is ignored, revealing a neural marker for the instant when the mind is made up.

rdcu.be/eGUrv

Transitions in dynamical regime and neural mode during perceptual decisions - Nature

Simultaneous recordings were made of hundreds of neurons in the rat frontal cortex and striatum, showing that decision commitment involves a rapid, coordinated transition in dynamical regime and neura...

www.nature.com

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Reposted by Julie Fabre

Guido Meijer @guidomeijer.com · Aug 29

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...

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…

www.sciencedirect.com

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Reposted by Julie Fabre

Ilana Witten @ilanawitten.bsky.social · Aug 5

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!

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Reposted by Julie Fabre

Matteo Carandini @carandinilab.net · Jul 7

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...

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Julie Fabre @juliefabre.bsky.social · Jun 24

Congrats!! 🎉

Julie Fabre @juliefabre.bsky.social · Jun 16

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 :)

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Reposted by Julie Fabre

Matteo Carandini @carandinilab.net · Jun 9

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...

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 ...

www.biorxiv.org

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Julie Fabre @juliefabre.bsky.social · Jun 13

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

Julie Fabre @juliefabre.bsky.social · Jun 13

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

Julie Fabre @juliefabre.bsky.social · Jun 13

📈 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

Julie Fabre @juliefabre.bsky.social · Jun 13

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.

Julie Fabre @juliefabre.bsky.social · Jun 13

📊 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.

Julie Fabre @juliefabre.bsky.social · Jun 13

🔧 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.

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Julie Fabre @juliefabre.bsky.social · Jun 13

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

github.com

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Reposted by Julie Fabre

Armin Lak @laklab.bsky.social · Jun 11

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...

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Reposted by Julie Fabre

Antonio Falasconi @antofala.bsky.social · May 28

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...

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. 

www.nature.com

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Reposted by Julie Fabre

Open Neuroscience @open-neuroscience.com · May 9

🔊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

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Reposted by Julie Fabre

Carlos Brody @carlosbrody.bsky.social · May 7

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!

Searchable database of tangible benefits that federally-funded research gave us.

A crowd-sourced site. Health and Well-being. National Security. Prosperity.

publicusaresearchbenefits.com

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Reposted by Julie Fabre

Matteo Carandini @carandinilab.net · Apr 1

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...

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Reposted by Julie Fabre

Normale Sup @normalesup.bsky.social · Apr 15

🎓 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

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Reposted by Julie Fabre

Enny van Beest @ennyvb.bsky.social · Apr 14

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...

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

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Reposted by Julie Fabre

Chris Zimmerman @czimmerman.bsky.social · Apr 3

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...

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.

www.nature.com

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Reposted by Julie Fabre

UCL Faculty of Brain Sciences @uclbrainscience.bsky.social · Apr 2

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! 👏

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.

buff.ly

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Julie Fabre @juliefabre.bsky.social · Apr 10

Thank you, Laura!!