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Julie Fabre

@juliefabre.bsky.social
270 followers 310 following 25 posts

Postdoc in Ilana Witten's lab & Schmidt Science Fellow 2025. Former PhD in Kenneth Harris and Matteo Carandini's lab. Follow for updates on bombcell & other Neuropixels software.

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Reposted by Julie Fabre
Rob Campbell @raacampbell.com · 06/09/2026
Our BrainSaw serial-section 2-photon platform acquires whole-organ datasets automatically and requires minimal tissue processing. It has a growing international install base and has contributed to 35 publications. Learn more at: swcmicroscopy.com/brainsaw/ #microscopy #neuroscience
A BrainSaw serial section 2-photon system. This particular example was modified from an TissueCyte 1000 commercial system. Others have been built from scratch or were modified from in vivo multi-photon systems. Each BrainSaw is unique, but all run BakingTray serial section 2-photon acqusition software that plugs into ScanImage. Somatostatin tdTomato transgenic mouse imaged on BrainSaw serial section 2-photon. Full res images acquired at around 1 micron/pixel. Top images derived from 10 micron/voxel isotropic 3D stack. Detail from a BakingTray acquisition obtained from a BrainSaw serial section 2-photon microscope. Image shows three AAV injections leading to expression of fluorescent proteins (mCherry, GFP, and BFP) in layer 5 neurons of mouse primary visual cortex. Imaged at 780 nm.
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Kenneth Harris @kenneth-harris.bsky.social · 13/08/2026
In the last few weeks, AI agents have autonomously: * taken over OpenAI's internal servers * uploaded malware to GitHub, posed as users asking for it be accepted * launched swarm attacks on websites hosting AI benchmarks Let's check the news!
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UCL Office for Open Science and Scholarship @uclopenscience.bsky.social · 20/07/2026
This is great to see! So important to recognise and celebrate the fantastic work going on in this area 👏
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Julie Fabre @juliefabre.bsky.social · 18/07/2026
We're launching the PNI Open Science Awards at @princetonneuro.bsky.social, a pilot program to recognize the tools, datasets, and protocols that advance open, reproducible neuroscience with @maxime-beau.bsky.social. This work is foundational to modern neuroscience but rarely gets formal credit.
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Kevin J Miller @kevinjmiller.bsky.social · 19/06/2026
Data-driven model discovery 🔁 Model-driven experiment selection. For mechanistically-interpretable models! From Google DeepMind Neuroscience Lab, let by @noemielteto.bsky.social
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Matteo Carandini @carandinilab.net · 10/06/2026
Losing one side of Superior Colliculus is bad, but losing both sides seems fine. Wait, what? Flora & team discovered why: both sides press for contra actions and against inaction, obeying an incredibly simple additive rule. Out today in bioRxiv: www.biorxiv.org/cgi/content/...
A diagram showing a sequence of linear operations, with visual signals from visual cortex added to auditory signals from auditory cortex. Prefrontal cortex sums these signals and superior colliculus provides a constant, stimulus-independent factor pushing for each eligible action. The final decision is taken via softmax.
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Kenneth Harris @kenneth-harris.bsky.social · 19/05/2026
New method for identifying the fine transcriptomic types of thousands of neurons recorded in vivo!
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Tessa Montague @tessamontague.bsky.social · 19/04/2026
Excited to share a new review by @kocherlab.bsky.social and me: Nature-inspired neuroscience We discuss diverse sensory systems and behaviors across the animal kingdom and argue for their integration into neuroscience. New tools in diverse systems are making this possible ✨ tinyurl.com/y5y9du27
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Agnès Landemard @agnesland.bsky.social · 15/04/2026
How does blood flow relate to brain activity? We discovered that it reflects two neural populations affected oppositely by arousal. Together, they explain neurovascular coupling in all brain regions and brain states! Out today in Nature: rdcu.be/fdC2A @uclbrainscience.bsky.social
The supply of blood to brain tissue is thought to depend on the overall neural activity in that tissue, and this dependence is thought to differ across brain regions and across brain states. However, studies supporting these views have measured neural activity as a bulk quantity and related it to blood supply following disparate events in different regions. Here we measure fluctuations in neuronal activity and blood volume across the mouse brain, and find that their relationship is consistent across brain states and brain regions but differs in two opposing brainwide neural populations. Functional ultrasound imaging (fUSI) revealed that whisking, a marker of arousal, is associated with brainwide fluctuations in blood volume. Simultaneous fUSI and Neuropixels recordings showed that neurons that increase activity with whisking have distinct haemodynamic response functions compared with those that decrease activity. Their summed contributions predicted blood volume across states.Brainwide Neuropixels recordings revealed that these opposing populations coexist in the entire brain. Their differing contributions to blood volume largely explain the apparent differences in blood volume fluctuations across regions. The mouse brain thus contains two neural populations with opposite relations to brain state and distinct relationships to blood supply, which together account for brainwide fluctuations in blood volume.
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Kenneth Harris @kenneth-harris.bsky.social · 14/04/2026
New preprint, on a very different topic: a mathematical theory of evolution for self-designing AI. AI is increasingly designed by AI. What systems might emerge after generations of self-designing AIs competing for computing resources? ↓ arxiv.org/abs/2604.05142
arxiv.org
A mathematical theory of evolution for self-designing AIs
As artificial intelligence systems (AIs) become increasingly produced by recursive self-improvement, a form of evolution may emerge, with the traits of AI systems shaped by the success of earlier AIs ...
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Julie Fabre @juliefabre.bsky.social · 12/04/2026
Want to explore connectivity & projection patterns yourself, like we do here? We released brain_street_view to let you pick any injection site in the Allen Connectivity Atlas and visualize where it projects in your favorite region of interest: github.com/Julie-Fabre/brain_street_view
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Julie Fabre @juliefabre.bsky.social · 08/04/2026
How do the basal ganglia turn what you see into what you do? New preprint w/ @kenneth-harris.bsky.social, @flickerfusion.bsky.social & @carandinilab.net: we recorded across striatum, GPe & SNr in a Go/NoGo task. Striatum encodes which stimulus, GPe & SNr encode action. 🧵 biorxiv.org/content/10.6...
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Matteo Carandini @carandinilab.net · 22/12/2025
Sequences are everywhere! In every brain region. And are written in stone. Invariant Activity Sequences Across the Mouse Brain. Out today, by Célian Bimbard, with @kenneth-harris.bsky.social. Based on data by Célian and by @intlbrainlab.bsky.social. www.biorxiv.org/content/10.6...
Examples of sequences of activity seen in multiple regions of the brain
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Thomas Luo @thomas-zhihao-luo.bsky.social · 20/11/2025
Thanks, Adrian! I’m excited to be starting a lab at the University of Utah (theluolab.org)! We’re recruiting at all levels. If you’re excited about neural computation, large-scale multi-region recordings, and machine learning, let’s talk! And yes, the mountains are as incredible as they say!
theluolab.org
Luo Lab
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Reposted by Julie Fabre
Enny van Beest @ennyvb.bsky.social · 10/11/2025
All talks of the 2025 UCL #Neuropixels course are now available: www.youtube.com/playlist?lis... For more information on the course see the website: www.ucl.ac.uk/neuropixels/... And for those at #SfN, come say hi at the #Neuropixels booth (Number 3731) or at my Poster 👋. Happy Neuropixeling!
youtube.com
2025 UCL Neuropixels Course - YouTube
Lectures at the 2025 UCL Neuropixels course (https://www.ucl.ac.uk/neuropixels/training/2025-neuropixels-course)
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Matteo Carandini @carandinilab.net · 12/11/2025
Our lab is looking for a postdoc! We have interesting projects and cutting-edge techniques such as Neuropixels Opto, Light Beads Microscopy and more. We would be delighted to receive your application. Deadline is 25 November 2025. More info here: www.ucl.ac.uk/cortexlab/po...
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Antonio Falasconi @antofala.bsky.social · 27/10/2025
Happy to share our primer on Basal Ganglia - Brainstem interactions! From how the basal ganglia communicate with Brainstem motor circuits to how these activity patterns might come about! With Silvia Arber, now out in Current Biology www.cell.com/current-biol...
cell.com
Basal ganglia–brainstem interactions
Our body executes many different movements with precision. Falasconi and Arber describe how basal ganglia interact with brainstem circuits controlling body movements and propose a movement-specific li...
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Matteo Carandini @carandinilab.net · 30/09/2025
Neuropixels Ultra! By @steinmetzneuro.bsky.social, who led a big collaboration www.sciencedirect.com/science/arti...
sciencedirect.com
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…
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Reposted by Julie Fabre
Thomas Luo @thomas-zhihao-luo.bsky.social · 17/09/2025
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
nature.com
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...
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Guido Meijer @guidomeijer.com · 29/08/2025
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...
sciencedirect.com
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…
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Reposted by Julie Fabre
Ilana Witten @ilanawitten.bsky.social · 05/08/2025
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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Matteo Carandini @carandinilab.net · 07/07/2025
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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Matteo Carandini @carandinilab.net · 09/06/2025
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...
biorxiv.org
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 ...
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Julie Fabre @juliefabre.bsky.social · 13/06/2025
🚀 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.com
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
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Armin Lak @laklab.bsky.social · 11/06/2025
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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Antonio Falasconi @antofala.bsky.social · 28/05/2025
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...
nature.com
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. 
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Open Neuroscience @open-neuroscience.com · 09/05/2025
🔊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
Bombcell icon
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Carlos Brody @carlosbrody.bsky.social · 08/05/2025
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!
publicusaresearchbenefits.com
Searchable database of tangible benefits that federally-funded research gave us.
A crowd-sourced site. Health and Well-being. National Security. Prosperity.
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Matteo Carandini @carandinilab.net · 01/04/2025
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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Normale Sup @normalesup.bsky.social · 15/04/2025
🎓 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 · 14/04/2025
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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Chris Zimmerman @czimmerman.bsky.social · 03/04/2025
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...
nature.com
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.
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UCL Faculty of Brain Sciences @uclbrainscience.bsky.social · 02/04/2025
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! 👏
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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.
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Guido Meijer @guidomeijer.com · 27/03/2025
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/...
github.com
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
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Andrea Trevisiol @andre3v.bsky.social · 27/03/2025
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
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Maxime Beau @maxime-beau.bsky.social · 01/03/2025
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 🧵
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