Jure Majnik
@juremaj.bsky.social
PhD student in (developmental/comp)neuroscience. Cossart lab (INMED, Marseille). track2p.github.io
Pinned
Jure Majnik
@juremaj.bsky.social
· Mar 3
How does a neuron get its activity? 👀
Check out our latest preprint, where we tracked the activity of the same neurons throughout early postnatal development: www.biorxiv.org/content/10.1...
see 🧵 (1/?)
Check out our latest preprint, where we tracked the activity of the same neurons throughout early postnatal development: www.biorxiv.org/content/10.1...
see 🧵 (1/?)
Reposted by Jure Majnik
Our work on training biophysical models with Jaxley is now out in @natmethods.nature.com. Led by @deismic.bsky.social, with @philipp.hertie.ai, @ppjgoncalves.bsky.social & @jakhmack.bsky.social et al.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods
Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...
www.nature.com
November 13, 2025 at 1:08 PM
Our work on training biophysical models with Jaxley is now out in @natmethods.nature.com. Led by @deismic.bsky.social, with @philipp.hertie.ai, @ppjgoncalves.bsky.social & @jakhmack.bsky.social et al.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Reposted by Jure Majnik
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
November 12, 2025 at 2:41 AM
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
Reposted by Jure Majnik
Connectome datasets alone are generally not sufficient to predict neural activity. However, pairing connectivity information with neural recordings can produce accurate predictions of activity in unrecorded neurons
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Prediction of neural activity in connectome-constrained recurrent networks - Nature Neuroscience
The authors show that connectome datasets alone are generally not sufficient to predict neural activity. However, pairing connectivity information with neural recordings can produce accurate predictio...
www.nature.com
November 10, 2025 at 10:12 PM
Connectome datasets alone are generally not sufficient to predict neural activity. However, pairing connectivity information with neural recordings can produce accurate predictions of activity in unrecorded neurons
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jure Majnik
How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework?
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
November 10, 2025 at 6:46 AM
How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework?
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
Reposted by Jure Majnik
Conrad Hal Waddington was born OTD in 1905.
His “epigenetic landscape” is a diagrammatic representation of the constraints influencing embryonic development.
On his 50th birthday, his colleagues gave him a pinball machine on the model of the epigenetic landscape.
🧪 🦫🦋 🌱🐋 #HistSTM #philsci #evobio
His “epigenetic landscape” is a diagrammatic representation of the constraints influencing embryonic development.
On his 50th birthday, his colleagues gave him a pinball machine on the model of the epigenetic landscape.
🧪 🦫🦋 🌱🐋 #HistSTM #philsci #evobio
November 8, 2025 at 4:03 PM
Reposted by Jure Majnik
We have written two reviews providing a practical guide and fundamentals of cell migration:
(1) How to select an optimal cell migration assay,
(2) How to analyze cell migration data.
We also added a perspective on AI methods of analysis.
Coming out soon in Nature Methods.
(1) How to select an optimal cell migration assay,
(2) How to analyze cell migration data.
We also added a perspective on AI methods of analysis.
Coming out soon in Nature Methods.
November 8, 2025 at 6:17 PM
We have written two reviews providing a practical guide and fundamentals of cell migration:
(1) How to select an optimal cell migration assay,
(2) How to analyze cell migration data.
We also added a perspective on AI methods of analysis.
Coming out soon in Nature Methods.
(1) How to select an optimal cell migration assay,
(2) How to analyze cell migration data.
We also added a perspective on AI methods of analysis.
Coming out soon in Nature Methods.
Reposted by Jure Majnik
New issue of Nature - with NINE studies on #brain #development from the BRAIN Initiative Cell Atlas Network (BICAN) 🧠🧪🔬
An amazing set of resources for all scientists working on the brain!
🧠 Immersive feature:
www.nature.com/immersive/d4...
🧠 Perspective:
www.nature.com/articles/s41...
An amazing set of resources for all scientists working on the brain!
🧠 Immersive feature:
www.nature.com/immersive/d4...
🧠 Perspective:
www.nature.com/articles/s41...
November 5, 2025 at 6:53 PM
New issue of Nature - with NINE studies on #brain #development from the BRAIN Initiative Cell Atlas Network (BICAN) 🧠🧪🔬
An amazing set of resources for all scientists working on the brain!
🧠 Immersive feature:
www.nature.com/immersive/d4...
🧠 Perspective:
www.nature.com/articles/s41...
An amazing set of resources for all scientists working on the brain!
🧠 Immersive feature:
www.nature.com/immersive/d4...
🧠 Perspective:
www.nature.com/articles/s41...
Reposted by Jure Majnik
Do flies feel pain?
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
October 29, 2025 at 6:56 PM
Do flies feel pain?
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
Reposted by Jure Majnik
The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1
October 27, 2025 at 8:15 AM
The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1
Reposted by Jure Majnik
🧠🌟🐭 Excited to share some of my postdoc work on the evolution of dexterity!
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
October 22, 2025 at 8:41 PM
🧠🌟🐭 Excited to share some of my postdoc work on the evolution of dexterity!
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
Reposted by Jure Majnik
doi.org/10.1126/scie...
This seems rad: overexpressing FruM in a set of proboscis-motorneuron-projecting neurons makes melanogaster males add food-sharing to their courtship repertoire.
It is fascinating to see evolutionary shifts in behavior be tied so concretely to shifts in brain development!
This seems rad: overexpressing FruM in a set of proboscis-motorneuron-projecting neurons makes melanogaster males add food-sharing to their courtship repertoire.
It is fascinating to see evolutionary shifts in behavior be tied so concretely to shifts in brain development!
Cross-species implementation of an innate courtship behavior by manipulation of the sex-determinant gene
In accepting a courting male, Drosophila subobscura females require nuptial gift giving in which a male gives regurgitated crop contents to her mouth to mouth. No similar behavior is found in D. melan...
doi.org
October 20, 2025 at 2:39 AM
doi.org/10.1126/scie...
This seems rad: overexpressing FruM in a set of proboscis-motorneuron-projecting neurons makes melanogaster males add food-sharing to their courtship repertoire.
It is fascinating to see evolutionary shifts in behavior be tied so concretely to shifts in brain development!
This seems rad: overexpressing FruM in a set of proboscis-motorneuron-projecting neurons makes melanogaster males add food-sharing to their courtship repertoire.
It is fascinating to see evolutionary shifts in behavior be tied so concretely to shifts in brain development!
Reposted by Jure Majnik
Don’t forget the umlaut! Did you know the wild-type strain ‘Tu’ came from a pet shop in the German town of Reutlingen, a nearby city of Tübingen? This area was one of the sites of “The Big Screen” co-led by Christiane Nüsslein-Volhard in the 1990s. #ZebrafishFunFacts @maxplanckcampus.bsky.social 🧪
October 18, 2025 at 11:21 AM
Don’t forget the umlaut! Did you know the wild-type strain ‘Tu’ came from a pet shop in the German town of Reutlingen, a nearby city of Tübingen? This area was one of the sites of “The Big Screen” co-led by Christiane Nüsslein-Volhard in the 1990s. #ZebrafishFunFacts @maxplanckcampus.bsky.social 🧪
Reposted by Jure Majnik
great thread on the idea that a bunch of phenotype variability is not just nature vs nuture, but nature vs nature vs... randomness
Great review on The Genetics of Human Handedness: Microtubules and Beyond www.cell.com/trends/genet... - handedness is such an interesting phenotype!
Genetics of human handedness: microtubules and beyond
Handedness (i.e., the preference to use either the left or the right hand for fine
motor tasks) is a widely investigated trait. Handedness heritability is consistently
estimated to be 25%. After decad...
www.cell.com
October 18, 2025 at 10:42 AM
great thread on the idea that a bunch of phenotype variability is not just nature vs nuture, but nature vs nature vs... randomness
Very grateful for the opportunity to present at Bernstein 2025 + an amazing conference overall 😊 @bernsteinneuro.bsky.social
For anyone interested in the data here is the link to Zenodo:
zenodo.org/records/1709...
And the (almost final version of) the paper:
elifesciences.org/reviewed-pre...
For anyone interested in the data here is the link to Zenodo:
zenodo.org/records/1709...
And the (almost final version of) the paper:
elifesciences.org/reviewed-pre...
🧠 #BernsteinConference 2025 — Day 4 Recap
The final day featured 4 Invited Talks and 3 Contributed Talks, wrapping up an inspiring week of #CompNeuro discussions.
Thanks to all speakers and participants — we can’t wait to see you again next year!
#BernsteinNetwork
The final day featured 4 Invited Talks and 3 Contributed Talks, wrapping up an inspiring week of #CompNeuro discussions.
Thanks to all speakers and participants — we can’t wait to see you again next year!
#BernsteinNetwork
October 11, 2025 at 9:47 AM
Very grateful for the opportunity to present at Bernstein 2025 + an amazing conference overall 😊 @bernsteinneuro.bsky.social
For anyone interested in the data here is the link to Zenodo:
zenodo.org/records/1709...
And the (almost final version of) the paper:
elifesciences.org/reviewed-pre...
For anyone interested in the data here is the link to Zenodo:
zenodo.org/records/1709...
And the (almost final version of) the paper:
elifesciences.org/reviewed-pre...
Reposted by Jure Majnik
Reposted by Jure Majnik
Exciting news for #drosophila #connectomics and #neuroscience enthusiasts: the Drosophila male central nervous system connectome is now live for exploration. Find out more at the landing page hosted by our Janelia FlyEM collaborators www.janelia.org/project-team....
Male CNS Connectome
A team of researchers has unveiled the complete connectome of a male fruit fly central nervous system —a seamless map of all the neurons in the brain and nerve cord of a single male fruit fly and the ...
www.janelia.org
October 5, 2025 at 3:40 PM
Exciting news for #drosophila #connectomics and #neuroscience enthusiasts: the Drosophila male central nervous system connectome is now live for exploration. Find out more at the landing page hosted by our Janelia FlyEM collaborators www.janelia.org/project-team....
Reposted by Jure Majnik
Un-frigging-believable. I have waited for something like this for so long!
October 5, 2025 at 8:01 AM
Un-frigging-believable. I have waited for something like this for so long!
Reposted by Jure Majnik
Latest imaging data from our completely re-designed ExA-SPIM system.
Expansion-assisted imaging (3X expansion, 0.3 NA) enables brain-wide imaging with high-contrast and <400 nm effective resolution.
Expansion-assisted imaging (3X expansion, 0.3 NA) enables brain-wide imaging with high-contrast and <400 nm effective resolution.
September 29, 2025 at 4:04 PM
Latest imaging data from our completely re-designed ExA-SPIM system.
Expansion-assisted imaging (3X expansion, 0.3 NA) enables brain-wide imaging with high-contrast and <400 nm effective resolution.
Expansion-assisted imaging (3X expansion, 0.3 NA) enables brain-wide imaging with high-contrast and <400 nm effective resolution.
Reposted by Jure Majnik
🧵1/14 Preprint thread! Can we predict a cell’s fate based on its dynamics? 🔮 Our new study unveils a framework for watching development unfold in real-time, revealing how a cell's shape and movement encode info about its future fate. 🔬📄 Preprint: tinyurl.com/4shf8v4x
September 22, 2025 at 9:37 AM
🧵1/14 Preprint thread! Can we predict a cell’s fate based on its dynamics? 🔮 Our new study unveils a framework for watching development unfold in real-time, revealing how a cell's shape and movement encode info about its future fate. 🔬📄 Preprint: tinyurl.com/4shf8v4x
Reposted by Jure Majnik
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:32 AM
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
📄 arxiv.org/pdf/2507.01009 (1/N)
Reposted by Jure Majnik
Preprint -
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
September 8, 2025 at 4:25 PM
Preprint -
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
Reposted by Jure Majnik
So how did it work out? Well, some things went well and others not so well. We published a paper with our results and reflections on the process. If you're interested in spiking neural networks, sound localisation, or anarchist science, check it out: www.eneuro.org/content/12/7...
Spiking Neural Network Models of Interaural Time Difference Extraction via a Massively Collaborative Process
Neuroscientists are increasingly initiating large-scale collaborations which bring together tens to hundreds of researchers. At this scale, such projects can tackle big challenges and engage diverse p...
www.eneuro.org
September 4, 2025 at 2:59 PM
So how did it work out? Well, some things went well and others not so well. We published a paper with our results and reflections on the process. If you're interested in spiking neural networks, sound localisation, or anarchist science, check it out: www.eneuro.org/content/12/7...
Reposted by Jure Majnik
I rarely dive into circuit-mapping papers, but this blockbuster from @ribeirocarlitos.bsky.social lab is a doozy! Check it out.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
From Sensory Detection to Motor Action: The Comprehensive Drosophila Taste-Feeding Connectome
In Drosophila , the gustatory system is distributed across multiple body parts and tightly couples sensory input to value-based behaviors such as feeding, foraging, and social interactions. Despite th...
www.biorxiv.org
September 1, 2025 at 4:56 PM
I rarely dive into circuit-mapping papers, but this blockbuster from @ribeirocarlitos.bsky.social lab is a doozy! Check it out.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jure Majnik
Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
August 2, 2025 at 2:30 PM
Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Reposted by Jure Majnik
Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social in 2023. journals.biologists.com/dev/article/...
August 4, 2025 at 6:42 AM
Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social in 2023. journals.biologists.com/dev/article/...