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Jakob Troidl

@jakobtroidl.bsky.social
67 followers 100 following 6 posts

ai scientist @janelia • @harvard cs phd • ml / image analysis / connectomics

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Reposted by Jakob Troidl
Davi Bock @dddavi.bsky.social · 24/09/2026
Now I can say: last week we received Notice of Award from NSF on a Midscale Research Infrastructure Design proposal for a National Connectomics and Ultrastructure Volume Observatory (NCUVO) www.uvm.edu/uvmnews/news...
uvm.edu
UVM Launches $19 Million National Observatory to Unlock…
| The University of Vermont
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Misha Ahrens @mishaahrens.bsky.social · 09/09/2026
Whole-body cellular activity imaging in zebrafish, headed by Virginie Ruetten @vmsruetten.bsky.social - new paper is out: www.nature.com/articles/s41...
nature.com
Imaging cellular activity across all organs reveals body-wide circuits - Nature
An imaging system developed to record cellular activity throughout the whole body of zebrafish captures cellular organ dynamics and identifies multiple distributed circuits.
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HHMI @hhmi-science.bsky.social · 03/09/2026
(1/2) When Janelia set out to map every neuron in the fly brain in 2008, many thought it couldn’t be done. Nearly 20 years later, a complete wiring diagram of the 166,000+ neurons of the adult male fruit fly is helping to reveal the brain’s secrets: bit.ly/4zT7jPf.
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Zhihao Zheng @zhihaozheng.bsky.social · 07/08/2026
Happy to share the CA3 dataset is published. First large-scale dense connectomics from hippocampus. First connectomic dataset imaged in @princetonneuro.bsky.social. A harbinger of many larger datasets to come (for both). doi.org/10.1038/s415... #hippocampus But my personal favorite is (1/2)
doi.org
Hippocampal CA3 connectomics reveals a gradient of mossy fiber inputs and selective feedforward inhibition onto pyramidal cells - Nature Neuroscience
The authors present a dense connectomic reconstruction of a 0.1 mm3 hippocampal CA3 volume and reveal spatial gradients, high convergence and cell-type-selective feedforward inhibition of inputs to py...
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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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Justin Ellis-Joyce @justinellis-joyce.bsky.social · 09/06/2026
I was delighted to contribute to this amazing work lead by @asbates.bsky.social, Lee and Wilson labs, and a village of contributors. This is a monument complete with connections to muscles and proprioceptors which will enable us to simulate of the sensorimotor loops of a brain for the first time!!
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Martin Weigert @maweigert.bsky.social · 04/06/2026
Heading to #CVPR2026 in Denver, where we'll present our highlighted poster: "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" enabling joint processing of local/global views. youtu.be/apFzMgmUUnM Friday 5th, 4pm Poster session 2 #602 Led by @albertdm.bsky.social
youtu.be
MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy
YouTube video by Albert Dominguez Mantes
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Jakob Troidl @jakobtroidl.bsky.social · 27/05/2026
📢 We're recruiting AI Scientists at HHMI Janelia. I'm biased, but these are exceptional opportunities. You'd join as an independent scientist with access to excellent computational infrastructure, some of the best biological data in the world, and a vibrant collaborative environment.
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Jakob Troidl @jakobtroidl.bsky.social · 27/05/2026
Looking forward to speak at the BioImage Computing Workshop at ECCV in Malmö this year!
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Adam Marblestone @adammarblestone.bsky.social · 24/04/2026
zenodo.org/records/1969...
zenodo.org
How to obtain a complete human connectome at synaptic resolution within the next decade
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Konrad Kording @kordinglab.bsky.social · 31/03/2026
Preprint out arguing that we should build the techology to translate (compile) molecularly annotated connectomes into dynamics. I think this is incredibly important. arxiv.org/abs/2603.25713
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Janelia Conferences @janeliaconf.bsky.social · 18/02/2026
📢 Applications are open! This meeting brings together scientists using data-driven #AI to analyze + model neural circuits and uncover how the brain performs complex computations. 🧠 Apply by May 28 ➡️ janelia.news/NAI26 @computingnature.bsky.social @sinzlab.bsky.social @srinituraga.bsky.social
janelia.news
Data-Driven AI for Neuroscience
Organizers Carsen Stringer, HHMI/Janelia Research Campus Srini Turaga, HHMI/Janelia Research Campus Atika Syeda, HHMI/Janelia Research Campus Fabian Sinz, University of Göttingen Alice Wang,
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Ziv Epstein @ziv-e.bsky.social · 25/03/2026
Pleased to share our new paper forthcoming in @icwsm.bsky.social! We introduce a novel framework to measure value expressions in social media posts at scale, leveraging personalization to handle the inherent subjectivity of human values. arxiv.org/abs/2511.08453
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Virginie Uhlmann @virginieuhlmann.bsky.social · 15/03/2026
Check out @cfusterbarcelo.bsky.social's latest cool work! Domain shift, we are watching you 👀👀👀
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Cedric Allier @allierced.bsky.social · 10/03/2026
Graph neural networks recover interpretable circuit models from neural activity saalfeldlab.github.io/flyvis-gnn/ @HHMIJanelia @AllenInstitute to be presented at @CosyneMeeting
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Linda Ulmer @lulmer.bsky.social · 11/03/2026
Looking forward to presenting our work on connectome-constrained modeling at #cosyne2026
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Reposted by Jakob Troidl
Konrad Kording @kordinglab.bsky.social · 11/03/2026
In two hours we (with gunnar blohm and jordan matelsky) will run a webinar talking about our philosophy for doing good science and becoming good at science. And the tool planyourscience.com I wrote to help. If you want to join us you can sign up here:t.co/OJOQe1Ly18
planyourscience.com
Scientific Paper Planner - AI-Powered Research Planning
Structure your scientific research with AI-powered guidance. From hypothesis to methodology, plan your research paper with intelligent mentoring.
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Jakob Troidl @jakobtroidl.bsky.social · 10/03/2026
Made it across the pond to Heidelberg for the AI & Biology conference at EMBL, then Lisbon for COSYNE. Looking forward to catching up with people and talking connectomics, AI for bio-image analysis, and more.
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Jan Funke @janfunkey.bsky.social · 05/03/2026
We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see 👇). My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue. Apply by March 26.
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Casey Schneider-Mizell @csdashm.com · 20/02/2026
From @bdpedigo.bsky.social: a super efficient, highly reliable, and very generalizable method for mesh structure classification, applied here to spine detection across basically every synapse onto a cell in the MICRoNS dataset.
Mesh analysis pipeline showing feature extraction and spine classification.
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Stephan Saalfeld @herrsaalfeld.bsky.social · 26/02/2026
Join us in building foundational datasets and models for microscopy with @jakobtroidl.bsky.social and many others AI Engineer Pre-Training: lnkd.in/eyEEV5nm AI Engineer Post-Training: lnkd.in/eShVQ3y9 Data Engineer Data: lnkd.in/eCvm58xH Data Engineer Pipelines: lnkd.in/ec6qGJkX ai.hhmi.org
ai.hhmi.org
Accelerating Innovation in Biology
HHMI’s $500 million over the next 10 years will support AI-driven projects and embed AI systems throughout the scientific process in labs across HHMI.
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