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Jure Majnik

@juremaj.bsky.social
314 followers 830 following 21 posts

PhD student in (developmental/comp)neuroscience. Cossart lab (INMED, Marseille). track2p.github.io

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Reposted by Jure Majnik
HHMI @hhmi-science.bsky.social · 11/10/2026
Every cell has an organelle signature — a “fingerprint” created from the shape, size, & arrangement of its internal structures. Scientists at our Janelia Research Campus can now read these signatures across 1000s of cells, revealing how tissues adapt to diet & disease bit.ly/4j6DmoH 📹 Feliciano Lab@
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Jill Oberski, PhD @jilloberski.bsky.social · 05/02/2026
Hey bsky! I’d like to share some cool work I recently coauthored that integrates entomology, paleontology, and German cultural history. 🔶🐜⚡️ We discovered a fossil ant in the amber collection of Johann Wolfgang von Goethe! Read on for a delightful story of #museomics and #collectomics. >> 1/
A 3D micro-CT scan of ant Ctenobethylus goepperti encased in amber
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Quanta Magazine @quantamagazine.org · 09/10/2026
In the mid 1900s, not everyone even believed that genes played a significant role in development. C.H. Waddington’s iconic epigenetic landscapes helped to change that. New data both confirms and complicates his ideas. www.quantamagazine.org/how-does-lif...
quantamagazine.org
How Does Life Unfold? A Landscape Metaphor Comes Into Its Own. | Quanta Magazine
C.H. Waddington’s powerful image of embryonic stem cells specializing on a rolling landscape has captivated biologists since the 1950s. Experimental data is finally confirming, and complicating, his v...
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Jure Majnik @juremaj.bsky.social · 06/10/2026
I can't imagine neuroscience without optogenetics ⚡️🔬🧑‍🔬 (an example from my work at Cossart lab, stimulating developing pyramidal neurons in vivo using the channelrhodopsin ChRmine developed by the Deisseroth lab) @deisseroth.bsky.social @nobelprize.org
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵
doi.org
From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence
Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...
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Rob Campbell @raacampbell.com · 04/10/2026
Preprint is out! Our BakingTray software turns a 2-photon microscope into a serial-section tomography system for automated whole-organ imaging. ~€35k to convert an existing scope. 11 systems worldwide, >7,000 samples at SWC alone #neuroskyence #microscopy www.biorxiv.org/content/10.6...
A BrainSaw at the Max Planck Institute for Brain Research, Frankfurt. A Nikon 16x water-immersion objective on a 400 µm travel PIFOC allows for fast z-stacks. Samples are imaged and cut in the clear water bath. A Leica VT1000 vibratome is seen to the right with a mounted blade.How BrainSaw works. Samples are embedded in an agarose block, which is glued to a slide and clamped into a water bath. The bath sits on a three-axis stage under a 2-photon microscope; the stage moves the sample for both tile scanning and slicing. The microscope images the exposed face of the block, the vibratome cuts off the imaged layer, and the cycle repeats until the samples have been fully imaged. Data are stitched automatically and are ready for downstream analysis. Logos below: BrainSaw (hardware), BakingTray (acquisition software), StitchIt (stitching).Coronal section of an Sst-tdTomato mouse brain imaged on BrainSaw. tdTomato-expressing cells are shown in yellow, scattered through cortex and hippocampus; tissue autofluorescence is shown in blue.Coronal section of a mouse brain with three neighbouring viral injections targeting layer 5 of V1, expressing mCherry (red), eGFP (green) and BFP (blue). The thick apical dendrites of the labelled neurons are clearly visible, as are their axons projecting to distant targets. Image credit: Alex Fritzl.
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Martin Haesemeyer @haesemeyerlab.bsky.social · 01/10/2026
CLOK: Truly beautiful new #zebrafish tool for birthdating neurons from the Koyama and Del Bene labs doi.org/10.1038/s415...
doi.org
CLOK: a chemigenetic multicolor labeling system to visualize neuronal birthdate and circuit integration - Nature Neuroscience
Faini et al. develop CLOK, a method that labels neurons across a spectrum of colors according to when they were born, allowing successive generations of brain cells to be tracked as they take shape in...
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Jason Rasgon @vectorgen.bsky.social · 30/09/2026
I am going to be buried with all my data, like the Pharaohs of old
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Pierre de Villemereuil @pdevillemereuil.bsky.social · 28/09/2026
With fieldwork, I didn't get to advertise our (not so now) new paper on the quantitative genetics of growth in the 🦎 in @journal-evo.bsky.social: dx.doi.org/10.1093/evol... It's an exciting paper paper in which we disentangle what it means to treat the whole growth curve as a function-valued trait!
dx.doi.org
Quantitative genetics of lifetime growth curves in a lizard
Abstract. Body size is an iconic trait in quantitative genetics. For species with indeterminate growth however, growth curve, a function-valued trait, is t
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epithelial mechanics fan club @epimechfc.bsky.social · 27/09/2026
Can mathematics explain how biological patterns are formed? Alan Turing thought so. Join me, @benswedlund.bsky.social , as we explore his reaction-diffusion theory and how it transformed our understanding of pattern formation and self-organisation.
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Rainer Friedrich @rainerfriedrichlab.bsky.social · 26/09/2026
Precise structural and functional organization of the olfactory bulb neuropil early in development, revealed by volume EM, dense reconstruction and 2P calcium imaging in zebrafish. Great work by Ruth and others in collaboration with @michalwj.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Fine ultrastructural organization of glomerular neuropil in the developing zebrafish olfactory bulb
Across animal phyla, odor information is represented in the first olfactory processing center by combinatorial activation of discrete glomeruli. To examine how this organization of olfactory processin...
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Reposted by Jure Majnik
Greg Priest @gregpriest.bsky.social · 25/09/2026
Thomas Hunt Morgan was born OTD in 1866. If you're ever feeling that your work is uending and unedifying, remember that he once said this: "Two years work wasted, I have been breeding those flies for all that time and I've got nothing out of it." 🌱🐋🧪 #HistSTM
Photograph of Morgan's Fly Room at Columbia University, around 1920. American Philosophical Society.
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The Transmitter @thetransmitter.bsky.social · 25/09/2026
How does the developing nervous system produce so many kinds of neurons? Two studies in flies reveal transcription-factor codes linked to neurons’ lineage and birth order. By Alissa de Chassey www.thetransmitter.org/development/...
thetransmitter.org
Fly neurons carry molecular signatures of their origins
The transcription factors a <em>Drosophila</em> neuron expresses offer clues to its lineage and birth order—and ultimately how neural circuits emerge.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Ann Kennedy @antihebbiann.bsky.social · 22/09/2026
We are very excited to use this method to study analytically how the interaction between neural activity and plasticity rules sculpts the dynamic landscape of a network in time-- for example to steer a developing circuit towards different architectures. Check it out! arxiv.org/abs/2609.22597
arxiv.org
Deviations from global coupling in adaptive oscillator networks: a mean-field theory for the variance of coupling weights
A wide range of physical and biological systems are adaptive networks, in which the dynamics of the nodes and of the edges connecting them co-evolve. Mean-field reductions of such systems typically tr...
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Jay Gallagher @jay-gallagher.bsky.social · 15/09/2026
🐟🚨 New paper! 🚨🐟 Where do behavioral differences come from? Early life environment clearly matters... ...or not? Early environment affected behavior, but NOT how different individuals became from each other. Those differences were seeded before birth through factors OTHER than genetic variation 🤯
onlinelibrary.wiley.com
Born This Way: Individuality Is Seeded Before Birth and Robust to Ecological Stress
We reared and recorded behaviours of clonal Amazon mollies in standardized environments, with and without predation stress, from birth through week four of life, to understand how the developmental e...
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John Tuthill @tuthill.bsky.social · 15/09/2026
yes, we can recognize pretty much all the same cell types across the existing fly connectomes. the new male CNS pape quantifies this. network topology between cell types is highly conserved, but synapse counts vary across datasets, likely due to reconstruction noise.
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domi @domi.zip · 09/09/2026
imagine you are killed while your brain is scanned by beings you cannot comprehend to comprehend and you wake up in a virtual purgatory waving swords around
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HHMI @hhmi-science.bsky.social · 09/09/2026
An animal’s body is in constant conversation with itself — & HHMI Janelia scientists have built a way to listen in. WHOLISTIC simultaneously records real-time activity from nearly every cell in a living larval zebrafish, a 1st step in understanding more complex bodies like ours: bit.ly/4xMR1Ww.
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Dr. Or M. Bialik |📚|🔬|🌊|⚒️ @obialik.bsky.social · 03/09/2026
Fish with electrical senses have unique brain cells specifically to process that information. The real trick they pull is separating the electricity they emit from the ones they sense. 🧪 Link: www.nature.com/articles/s41586-026-…
a, Schematic of the interference problem facing the passive electrosensory system of weakly electric fish. Responses of EAFs to prey are masked by responses to the EOD of the fish, which vary depending on factors such as water conductivity. b, Schematic of prediction and cancellation of responses to the EOD. Predictions are based on electric organ corollary discharge signals conveyed by GCs (granule cell basis) and require specific patterns of synaptic connectivity. c, Summary diagram of the synaptic connectivity patterns revealed in the present study. Only connections comprising >10% of the total synapses to a given cell type are shown in the diagram. d, Two example Output cells (blue and red) are shown along with EAF (pink) and GC (magenta) inputs overlaid on a cutout of the EM volume (424 × 427 × 45 µm; all EM connectomic data are from a single biological specimen). The dorsal–ventral and anterior–posterior dimensions of the skin surface are mapped onto the x- and z-dimensions of the volume, respectively. The top inset shows example excitatory GC synapses (magenta fill and star) onto apical dendritic spines of the ON cell (red fill). The magenta fill marks the example GC axon visualized in the volume; the magenta star marks another GC axon. The white star marks an inhibitory molecular layer interneuron synapse onto the dendritic shaft of the same ON cell. The bottom inset shows an example excitatory EAF synapse (pink fill) onto the ON cell basal dendrite (red fill). mol, molecular layer; ggl, ganglion layer; plex, plexiform layer; gran, granular layer. e–h, Example reconstructions of major ELL cell types. Axons are shown in black. ON/OFF, Output (h); MG+/MG−, medium ganglion (f); SG+/SG−, small ganglion (g); Gr+, granular; SP−, small plexiform (h). The inset in f shows an example inhibitory synapse between an MG+ cell (orange) and an OFF cell soma (blue).
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Kevin Mitchell @wiringthebrain.bsky.social · 03/09/2026
"In total, the male CNS connectome contains 166,700 neurons which form 11,710 cell types that can be identified across animals."
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Peter Rupprecht @ptrrupprecht.bsky.social · 18/08/2026
Interesting work from the lab of Na Ji on how axial imaging resolution (3.5- 20 um) affects the extraction of accurate neuronal signals. Very instructive! www.biorxiv.org/content/10.6...
biorxiv.org
High Axial Resolution Is Necessary for Quantitative Two-Photon Calcium Imaging of Neuronal Populations
Two-photon calcium imaging is a standard tool for measuring neuronal population activity in vivo , yet how axial resolution, sensor expression strategy, and analysis pipeline jointly affect data accur...
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Kirsty Wan @micromotility.bsky.social · 17/08/2026
What does a single-celled organism tell us about the origins of complex behaviour? Delighted to see the final version of our paper: Embodied behavioural complexity in a ciliated microorganism out in@natcomms.nature.com (Funded by @erc.europa.eu ERC) doi.org/10.1038/s414... #cilia #protistsonsky
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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 09/08/2026
Light sheet fluorescence microscopy (LSFM) movie of axon branching during #zebrafish development in a neurodegenerative disease gene (KLC4) mutant. Credit to @drlizhaynes.bsky.social. #ZebrafishZunday
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Peter Rupprecht @ptrrupprecht.bsky.social · 07/08/2026
Excited to share our work now in Nature Methods! We wrote this manuscript to help others better analyze and interpret calcium imaging data. As a central aspect, we show why nonlinear behavior of calcium indicators matters in practice. Very happy about this work!
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Kevin Mitchell @wiringthebrain.bsky.social · 05/08/2026
Cortical territories compete in developmental space race doi.org/10.53053/HIF...
doi.org
Cortical territories compete in developmental space race
Sensory and association regions are established through a reciprocal process, according to a new model of cortical development.
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Spencer LaVere Smith @spencerlaveresmith.bsky.social · 25/07/2026
Two-photon calcium imaging. What makes for good data? How can we optimize experiments to get good data? New post labrigger.com/blog/2026/07... and new free web apps from @filip-tomaska.bsky.social (1/8)
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Jure Majnik @juremaj.bsky.social · 24/07/2026
I'm not sure since I don't work on that, but based on the second paper (Lee et al. 2026) it should be possible I guess. They implant in rats at P6 (fig2) so I don't think mice P0 would be much more complex. Embryonically would probably be much more tricky though + getting the signal out somehow...
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Jure Majnik @juremaj.bsky.social · 23/07/2026
Thanks :) :) :)
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Jure Majnik @juremaj.bsky.social · 23/07/2026
and for imaging you can check my paper ;) elifesciences.org/articles/107... I cant speculate on the ephys part but here I would say within the next few years it should be possible to image the same cells from around birth to adulthood.
elifesciences.org
Longitudinal tracking of neuronal activity from the same cells in the developing brain using Track2p
A novel algorithm allowed for the continuous tracking of neurons throughout early postnatal development, revealing a transition in neural firing statistics coinciding with the onset of behaviour-depen...
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Jure Majnik @juremaj.bsky.social · 23/07/2026
you should check these: Sheng et al. 2025: Brain implantation of soft bioelectronics via embryonic development www.nature.com/articles/s41... Lee et al. 2026: Growth-adaptive spring electronics for long-term, same-neuron mapping in the developing rat brain www.biorxiv.org/content/10.6...
nature.com
Brain implantation of soft bioelectronics via embryonic development - Nature
A soft mesh microelectrode array can seamlessly integrate in developing brains, enabling long-term, stable mapping of how single-neuron activity and population dynamics emerge and evolve during brain ...
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 22/07/2026
In brain development, timing is everything. @sebastiancachero.bsky.social @erikadona.bsky.social & @jefferis.bsky.social have mapped 450,000+ cells from developing fly nervous systems to build an expansive atlas, revealing how neurons 'remember' when they were born. shorturl.at/tfI4s #LMBResearch🧪
Heatmap shows temporal expression of 17 transcription factors across neuron birth orders, with a UMAP plot visualising cell identity relationships.
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MwahahahahahadScientist @mads100tist.bsky.social · 21/07/2026
May I suggest Yinan's paper for the "scarce labeled datasets" bottleneck (basically, using tracking to infere future state, then use tracking to map it back to the previous state. We called it weMERFISHfate) www.science.org/doi/10.1126/...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Ricardo Henriques @henriqueslab.bsky.social · 21/07/2026
🚀🔬 Can cell shape, signal and movement tell us about a cell's future? #DeepLearning studies now predict cell fate from #microscopy. Together w Rita, @mariodelr.bsky.social, @inesmcunha.bsky.social, @juliettegriffie.bsky.social + @guijacquemet.bsky.social👇 www.preprints.org/manuscript/202607.1414/v1
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Alfonso Martinez Arias @amartinezarias.bsky.social · 14/07/2026
In the midst of foundational models of the cell (or should I say pseudocell), seen as an “bag”, this www.cell.com/cell/fulltex... is a great antidote, and one that anyone who knows that a cell is more than its genes, can relate to and understand #RealCellsRUs #NotInTheGenes
cell.com
Establishing a conceptual framework for holistic cell states and state transitions
Technological advances have brought “big data” to the cellular level. Rafelski and Theriot share their vision of defining a cell's state in a holistic way that reflects all molecular, organizational, ...
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FocalPlane @focalplane.bsky.social · 01/07/2026
Bringing together science & art, @manuelthery.bsky.social & the CytoMorpho lab describe their project on how cells adapt their shape to their environment using the Musée d’Orsay as their template! The full performance was presented over two nights at the museum earlier this year. #sciart #cellbio
focalplane.biologists.com
Living Architectures - FocalPlane
Living Architectures - Case studies
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Meike van der Heijden @meikeesther.bsky.social · 17/06/2026
New Preprint: Competitive Olivocerebellar Input Selection Promotes Resilient Circuit Formation -- Join the ride for some developmental neuroscience, stay for some pretty pictures. doi.org/10.64898/202...
doi.org
Competitive Olivocerebellar Input Selection Promotes Resilient Circuit Formation
Many neural circuits undergo competitive input selection, a process in which supernumerary connections compete for innervation territory on target cells. This process can create atypical circuits when...
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Mike Dorrity @mwdorr.bsky.social · 19/06/2026
First pre-print from the lab, a collaborative effort led by Jess Bourn @bournsupremacy.bsky.social, a fantastic PhD in my group. We resolve a key problem in development + evolution: how do we quantify heterochrony and link temporal variation to phenotype? www.biorxiv.org/content/10.6...
biorxiv.org
Quantitative mapping of heterochrony to species-specific phenotypes
The genetic program of animal development is conserved, but its rate of execution varies across species. Heterochrony, shifts in the relative timing of developmental events, generates phenotypic varia...
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eLife @elife.bsky.social · 19/06/2026
A fundamental study of individual variation and contribution of learning to behavioural individuality. Conclusions are supported by compelling, rigorous analysis across a number of experiments in thousands of individuals across genotypes and conditions.
buff.ly
Learning is a fundamental source of individuality
Altmetric provides a collated score for online attention across various platforms and media.See more details
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brunolemaitre.bsky.social @brunolemaitre.bsky.social · 17/06/2026
A short, informal intro to Drosophila genetics (with a French accent 🇫🇷): key concepts & techniques for new lab members. www.epfl.ch/labs/lemaitr...
epfl.ch
Short Introduction to Drosophila_Engl
If you like French accent:A short and informal introduction to Drosophila genetics, covering the basic knowledge and techniques that may be helpful when working with Drosophila. This series of short l...
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Bianca Dumitrascu @bimidu.bsky.social · 12/06/2026
How are two embryos alike? As we collect spatio-temporal microscopy data, we want to quantify variability in the timing of key developmental events. Alignment of multiple recordings is a core engineering challenge here and we suggest a solution; read about it: www.biorxiv.org/content/10.6...
biorxiv.org
A quantitative coordinate system for developmental dynamics
Quantitative comparison of morphogenesis across individuals remains a fundamental challenge, as developing embryos vary in shape, orientation and developmental tempo. Moreover, real-time three-dimensi...
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James Briscoe @jamesbriscoe.bsky.social · 08/06/2026
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Now published - the #BANC! A full central nervous system (CNS) connectome of a limbed animal at single-synapse resolution, enabling us to follow sensory-motor arcs and understand how the CNS controls the body. rdcu.be/fncjS. #neuroscience. Video by @quorumetrix.bsky.social 1/18
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Collège de France @college-de-france.fr · 08/06/2026
#Science #Biologie  🦇 « L’évolution des mécanismes du développement » 🖥️ Les vidéos du colloque organisé par le Pr @denisduboule.bsky.social, titulaire de la chaire #Évolution du développement et des #génomes, sont disponibles ! 👉 tinyurl.com/39p4h5pn
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 07/06/2026
Cortical folding patterns are encoded in the geometry of the unfolded neocortex. www.biorxiv.org/content/10.64898/20…
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Manu Leonetti @manu-leo.bsky.social · 03/06/2026
📣 new preprint multimodal atlas. Imaging + scRNA, 57M cells. 🧬🔬 Cells are complex dynamical systems — but most ways we measure them destroy them. We asked: how does live imaging compare to scRNA-seq, the field’s gold std? The answer surprised us 🧵 www.biorxiv.org/content/10.6...
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Ali Shaib @alishaib.bsky.social · 01/06/2026
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
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Ariel Levine @ariellevine.bsky.social · 29/05/2026
As someone interested in both genetics & neural activity, I appreciate the common challenge of linking causal function to system-level understanding. This excellent review by @jamesbriscoe.bsky.social & Maizels shows a way forward for gene networks in development pubmed.ncbi.nlm.nih.gov/41803457/
pubmed.ncbi.nlm.nih.gov
Gene regulatory networks: from correlative models to causal explanations - PubMed
Gene regulatory networks (GRNs) explain how the genome controls cellular behaviour and tissue morphogenesis, serving to connect molecular mechanism to functional output. Single-cell technologies now p...
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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 25/05/2026
“Using an optical backfilling method relying on photoactivable GFP, we generate a whole-brain map of all neurons sending axons towards the spinal cord. This approach reveals far more SPNs than previously described through conventional strategies.” Bonkers work from @wyartlab.bsky.social 🐟🧠
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Pawel Burkhardt @pawelburkhardt.bsky.social · 23/05/2026
A fossil nervous system meets modern neurobiology. We found that a living comb jelly preserves neural architecture remarkably similar to those inferred from Cambrian fossils over 500 million years old 🤩. www.biorxiv.org/content/10.6...
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