Julie Fabre
@juliefabre.bsky.social
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
https://github.com/Julie-Fabre
Pinned
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
🚀 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/...
pip install and play around with our toy dataset:
🔗 github.com/Julie-Fabre/...
Reposted by Julie Fabre
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!
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!
2025 UCL Neuropixels Course - YouTube
Lectures at the 2025 UCL Neuropixels course (https://www.ucl.ac.uk/neuropixels/training/2025-neuropixels-course)
www.youtube.com
November 10, 2025 at 1:48 PM
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!
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!
Reposted by Julie Fabre
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...
www.ucl.ac.uk/cortexlab/po...
November 12, 2025 at 3:41 PM
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...
www.ucl.ac.uk/cortexlab/po...
Reposted by Julie Fabre
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...
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...
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...
www.cell.com
October 27, 2025 at 8:49 PM
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...
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...
Reposted by Julie Fabre
Neuropixels Ultra!
By @steinmetzneuro.bsky.social, who led a big collaboration
www.sciencedirect.com/science/arti...
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
September 30, 2025 at 3:11 PM
Neuropixels Ultra!
By @steinmetzneuro.bsky.social, who led a big collaboration
www.sciencedirect.com/science/arti...
By @steinmetzneuro.bsky.social, who led a big collaboration
www.sciencedirect.com/science/arti...
Reposted by Julie Fabre
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
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
September 17, 2025 at 8:12 PM
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
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
Reposted by Julie Fabre
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...
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
August 29, 2025 at 10:00 AM
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...
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...
Reposted by 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!
Apply here: research-princeton.icims.com/jobs/21001/r...
Pls share w/ anyone who might be interested!
August 5, 2025 at 1:26 PM
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!
Apply here: research-princeton.icims.com/jobs/21001/r...
Pls share w/ anyone who might be interested!
Reposted by Julie Fabre
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...
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...
July 7, 2025 at 3:01 PM
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...
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...
Reposted by Julie Fabre
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
June 9, 2025 at 11:49 AM
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...
🚀 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/...
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
June 13, 2025 at 6:55 PM
🚀 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/...
pip install and play around with our toy dataset:
🔗 github.com/Julie-Fabre/...
Reposted by 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...
June 11, 2025 at 3:18 PM
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...
Reposted by Julie Fabre
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...
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
May 28, 2025 at 3:32 PM
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...
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...
Reposted by Julie Fabre
🔊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
💡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
May 9, 2025 at 5:36 PM
🔊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
💡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
Reposted by Julie Fabre
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
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
May 7, 2025 at 11:28 PM
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
please share and re-share so we get more great stories in there!
Reposted by Julie Fabre
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...
Suite3D: Volumetric cell detection for two-photon microscopy
by @haydari.bsky.social & team.
www.biorxiv.org/content/10.1...
April 1, 2025 at 11:10 AM
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...
Suite3D: Volumetric cell detection for two-photon microscopy
by @haydari.bsky.social & team.
www.biorxiv.org/content/10.1...
Reposted by Julie Fabre
🎓 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
À lire ici 👉 bit.ly/3Gm0RsA
April 15, 2025 at 3:00 PM
🎓 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
À lire ici 👉 bit.ly/3Gm0RsA
Reposted by Julie Fabre
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...
April 14, 2025 at 2:45 PM
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...
Reposted by Julie Fabre
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...
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
April 3, 2025 at 6:34 PM
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...
Our answer in @nature.com this week: Illness signals from the gut reactivate and strengthen flavor representations in the amygdala.
📄: nature.com/articles/s41...
Reposted by Julie Fabre
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! 👏
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
April 2, 2025 at 2:43 PM
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! 👏
Congratulations to both Dr @juliefabre.bsky.social & Dr Almarri on this incredible achievement! 👏
Reposted by Julie Fabre
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/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
March 27, 2025 at 10:38 AM
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/Julie-Fabre/...
Reposted by 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
March 27, 2025 at 4:42 PM
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
Reposted by Julie Fabre
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 🧵
March 1, 2025 at 1:14 PM
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 🧵