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Stephan Saalfeld

@herrsaalfeld.bsky.social
862 followers 148 following 73 posts

scalable data analysis, modeling, AI, software design at HHMI Janelia mastodon.social/@herrsaalfeld

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Reposted by Stephan Saalfeld
Gaspar Jekely @jekely.biologists.social.ap.brid.gy · 30/09/2026
If you are interested in serial sectioning for electron microscopy, we have now uploaded a revised version of our paper Shahidi et al: "Volume Electron Microscopy: Tips & Tricks on Micromanipulator-Assisted Serial Sectioning for Array Tomography" […] [Original post on biologists.social]
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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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Janelia FlyEM @janelia-flyem.bsky.social · 04/09/2026
We're thrilled with the publication of the Male CNS Connectome! www.cell.com/cell/fulltex... Also check out this (growing) collection of companion papers: www.cell.com/consortium/m...
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Leslie B Vosshall PhD @leslievosshall.bsky.social · 04/09/2026
"You've got to be in it to win it" Please consider applying to be one of our 2027 #GilliamFellows Biggest cohort ever n=80 fellows will be selected. So many of our current wonderful fellows almost didn't apply, and we are so glad that they did. Resources here: www.hhmi.org/programs/gil...
hhmi.org
PhD and Postdoc Transition Program | Gilliam Fellows | HHMI
The Gilliam Fellows Program supports PhD students and their faculty thesis advisors in advancing cutting-edge research and fostering inclusive scientific training environments, while supporting the tr...
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Tom Aarsen @tomaarsen.com · 03/09/2026
🤗💚I'm very excited to continue our open source and open weight journey together with NVIDIA! See the announcement here: blogs.nvidia.com/blog/nvidia-...
blogs.nvidia.com
NVIDIA to Acquire Hugging Face
NVIDIA has agreed to acquire Hugging Face. Together, we will scale Hugging Face’s platform, strengthen its infrastructure and expand access to AI for developers and institutions worldwide.
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Kit D. Longden @theflyside.bsky.social · 21/08/2026
Mosquito Aedes aegypti brain connectome project is super exciting: jobs available Elizabeth Marin & @jefferis.bsky.social recruiting Research Assistant and Postdoctoral Research Associate Deadline: 3 September 2026 Brilliant colleagues & bosses - highly recommend flyconnecto.me/2026/08/01/t...
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Dr. Allyson Sgro @allysonsgro.bsky.social · 21/08/2026
Interested in how cells communicate and process information to work together? Love microscopy and seeing things no human has seen before for the first time? Finishing up your Ph.D. or position in early 2027? We are looking for an experimental postdoc to join the lab. Please reach out!
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Memming Park @memming.bsky.social · 04/08/2026
Nothing in neural activity makes sense except in the light of dynamics and cybernetics. #CCN2026 GAC position. sites.google.com/ccneuro.org/...
sites.google.com
GACs - 2026-3
Representations or Transformations: What Should Models of Neural Population Activity Explain? Julian Kędys, Poznan Supercomputing and Networking Center Cezary Mazurek, Poznan Supercomputing and Netwo...
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paveltomancak.bsky.social @paveltomancak.bsky.social · 03/08/2026
www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
Multiple contact sites between cells and the vitelline envelope coordinate tissue flows in Drosophila gastrulation
Gastrulation is thought to be driven primarily by forces generated within individual cells. These cell-intrinsic forces collectively induce tissue-scale flows and transform the monolayered embryo into...
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Luke Lavis @rhodamine110.bsky.social · 17/07/2026
Excited to see this collaboration now in print. Dye chemistry meets AI-designed proteins. Three small, orthogonal tags; lifetime modulation; split versions. Request the free dyes at dyes.janelia.org www.science.org/doi/10.1126/...
science.org
De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging
Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostabilit...
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Stephan Saalfeld @herrsaalfeld.bsky.social · 18/07/2026
Not the moon.
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Reposted by Stephan Saalfeld
John Bogovic @bogovicj.bsky.social · 17/07/2026
It's an exciting day for #Fiji users! Now read and write @zarr.dev v3 and #OMEZarr v0.5. Don't want a million tiny files in your #zarr? Shard that sucker! Read the details here forum.image.sc/t/fiji-can-r...
forum.image.sc
Fiji can read and write Zarr3 & OME-Zarr v0.5 (new N5 release!)
Updating your Fiji-Latest installation will give you the newest versions of the N5 library, enabling OME-Zarr v0.5 / Zarr v3 support with sharding! What's new? Reading zarr 3 datasets (sharded and u...
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Christophe 🔬 Leterrier @christlet.bsky.social · 15/07/2026
Important for parents of (pre)-teens to keep in mind. Surveillance brings anxiety, trust begets trust
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Brad Hulse @bradkhulse.bsky.social · 21/05/2026
Story time friends... Ring attractor networks rely on fine-tuned symmetric connectivity. The fly head direction network has ring attractor dynamics but heterogeneous connectivity. How is this possible? 1/🧵 Link: www.biorxiv.org/content/10.6...
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 16/06/2026
With a motivating push from @christlet.bsky.social I made a new Fiji plugin, CurveMorph. The idea was to create a tool for kymograph generation along the dynamic (bending/shaking) filament shapes (microtubules, cilia, neurites, etc). The logo was made using the plugin. github.com/UU-cellbiolo...
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HHMI @hhmi-science.bsky.social · 15/06/2026
Janelia is built for this moment. Starting today, we're taking on 2 big bets: cracking how a vertebrate brain generates behavior, & building AI-in-the-Loop Discovery — a new way of doing biology. Tiny transparent fish + one of neuroscience’s biggest questions? Let's go: hhmi.news/2BigBets
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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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Venki Murthy @neurovenki.bsky.social · 29/05/2026
Nice piece in @theharvardcrimson.bsky.social about our @kempnerinstitute.bsky.social! I say a few things in it.
thecrimson.com
Harvard's Kempner Institute Bet Big on AI. Now It Has to Prove Itself. | News | The Harvard Crimson
Harvard’s Kempner Institute made an early bet on owning its own AI computing cluster — a gamble that has quickly made it a rare academic hub for artificial intelligence research, even as private indus...
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Miguel Nunez @nunezkant.bsky.social · 26/05/2026
1/ 🚨🚨Preprint alert! "Perfect" isn't always smart 🧠. Anyone can tell apart two stimuli (including our mice). But how do we extract rules that apply to new stimuli? 🧵 biorxiv.org/content/10.6... @marius10p.bsky.social @computingnature.bsky.social #neuroAI #neuroscience #AI
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 21/05/2026
New release of #BigVolumeBrowser (0.1.1) adds support for (multiscale) OME-Zarr (thanks to libraries from @bogovicj.bsky.social, Stefan Hahmann, Vladimir Ulman). And midi gizmo navigation (from @herrsaalfeld.bsky.social ), shown below.
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Kristin Branson @kristinmbranson.bsky.social · 18/05/2026
New preprint with @lingqiz.bsky.social: Neurodata Without Boredom: Benchmarking Agentic AI for Data Reuse arxiv.org/abs/2605.12808 1/10
Overview of the data conversion task. The benchmark includes eight datasets spanning a range of neural recording modalities, behavioral tasks, measurements, experiment protocols, and data formats. For each dataset, agents were also given the released paper, methods, and code, together with a structured prompt. The agent’s goal was to convert each heterogeneous source dataset into a common format suitable for a neural decoding task. 
Diagram has a column for each of 8 papers from mouse systems neuroscience. The first row shows the name of the dataset and a description of the focus of that work: 1) Allen2P: Visual change detection,2) Lee2025: Spatial coding & remapping, 3) Majnik2025: Cortical development, 4) Sosa2024: Spatial reward learning,  5) Chen2024: Memory-guided decision, 6) Hasnain2024: Context-based decision, 7) Zhang2025: Visual-motor decision, 8) Zhong2025: Visual learning. 
The next row shows the type of neural recording data: 1, 3, 4, 8: head-fixed calcium imaging, 2: miniprobe, 5-7: neuropixels or other silicon probes
The next row shows the types of behavioral and task variables. These are different for every task
The next row shows a visualization of the experiment protocol for each task. Again, these are different for every task
The next row shows that this information is all condensed into data, paper, and code. Data has the different types of information in different orders and structures. It also shows the type of files: 1: NWB files & SDK, 2,6: MATLAB files, 3, 7: Python files, 4-5: NWB files, 8: Various + API
The next part of the diagram shows the task, which is for agents to convert the data to a common data format for a downstream decoder task.
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Laura Grima @lauragrima.bsky.social · 09/05/2026
Really pleased that this work with @dudman.bsky.social is now out in Neuron: A global dopaminergic learning rate enables adaptive foraging across many options
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Friedemann Zenke @fzenke.bsky.social · 06/05/2026
1/7 New paper accepted as ICML spotlight arxiv.org/abs/2605.03517! We unify self-supervised learning (SSL) algorithms (e.g., contrastive, VICReg, stopgrad) via latent distribution matching (LDM), which matches an induced latent distribution to an explicit latent model.
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Ewerslab @ewerslab.bsky.social · 05/05/2026
New paper out! Left-handed DNA cannot bind to natural, right-handed DNA. This leads to lower background if it is used as a probe in DNA-PAINT. Using Fluorigenic DNA-PAINT with left-handed DNA allows for low background, fast 3D DNA-PAINT! Congrats, Bas! skeetorial: 1/x pubs.acs.org/doi/full/10....
pubs.acs.org
Accelerated Left-Handed DNA-PAINT Using Fluorogenic Probes
Single-molecule localization microscopy (SMLM) techniques offer nanometer-scale resolution by stochastically localizing individual fluorescent molecules. Among these, DNA-mediated point accumulation f...
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 30/04/2026
After 9 years, I am finally finishing the story about normalized cross-correlation (and reviving my blog). The new blog post about deep technical details on the most used image registration technique. I know y'all have been waiting. katpyxa.info/feedbacks/?p...
katpyxa.info
Calculating normalized cross-correlation (part 3) – //><=~!=//
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Marieke van Vugt @mvugt.bsky.social · 30/04/2026
"Warm models showed substantially higher error rates (+10 to +30 percentage points) than their original counterparts, promoting conspiracy theories, providing inaccurate factual information and offering incorrect medical advice. " rdcu.be/fgea6
rdcu.be
Training language models to be warm can reduce accuracy and increase sycophancy
Nature - Experiments on five different language models show that training language models to produce warmer responses can undermine the accuracy of their output, especially when users express...
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Franz Rieger @riegerfr.bsky.social · 21/04/2026
Can generative AI accelerate neuroscience? Excited to share MoGen at ICLR 2026!🧠 We use point cloud flow matching to generate high-fidelity 3D neuron fragments, capturing intricate details like dendritic spines.
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Current Biology @currentbiology.bsky.social · 18/04/2026
Eating its own tail, the central dogma of molecular biology has come full circle! 🧬
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John Tuthill @tuthill.bsky.social · 17/04/2026
New @currentbiology.bsky.social paper from Dr. Leila Elabbady on neural circuits that transform a touch stimulus into spatially targeted grooming. Leila discovered a leg somatotopic map and used it to infer tactile receptive fields in the fly VNC connectome. authors.elsevier.com/a/1mvu83QW8S...
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Luke Lavis @rhodamine110.bsky.social · 15/04/2026
Out in @natmethods.nature.com: More dyes. They work. Quite well. And blink. Pick the one that fits your target, your technique, and your labeling density. With too many collaborators and institutes to list, but anchored at @hhmijanelia.bsky.social www.nature.com/articles/s41...
nature.com
A series of spontaneously blinking dyes for super-resolution microscopy - Nature Methods
A series of spontaneously blinking dyes in the far-red range facilitate single-molecule localization microscopy. These dyes vary in their blinking properties and can be matched to the applications and...
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Oliver Rocks @oliverrocks.bsky.social · 15/04/2026
Check out our new release on BioRxiv co-lead by @pm-mueller.bsky.social 👉 rb.gy/lnrizk special🙏 to Severine Kunz #MDC @leventallab.bsky.social @andimicroscopy.bsky.social @ewerslab.bsky.social and Kedar Narayan @NCI CCR VolumeEM Are the days of discovering new cellular structures over?? /1
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Dr. Allyson Sgro @allysonsgro.bsky.social · 15/04/2026
Last call!
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European Commission @ec.europa.eu · 09/04/2026
Big opportunities for researchers 🌍 We are investing nearly €400 million to help researchers share their work and collaborate with the best scientific teams across the EU. The 2026 Marie Skłodowska-Curie Actions Postdoctoral Fellowships are now open. More: link.europa.eu/PNxpxw
Graphic announcing the MSCA Postdoctoral Fellowships 2026 call. It shows the opening date (9 April 2026), closing date (9 September 2026), and a budget of €399.05 million. The design features scientific visuals such as cells, a leaf, and lab elements on a dark background, with the European Commission logo at the bottom.
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Caitie McCafferty @computingcaitie.bsky.social · 08/04/2026
I am excited to share our most recent work collaborating with @centriolelab.bsky.social and @stearnslab.bsky.social to look at the ciliary base of mammalian multiciliated cells w/ cryo-ET, XL/MS, and U-ExM www.biorxiv.org/content/10.6...
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Janelia Conferences @janeliaconf.bsky.social · 02/04/2026
🚨 Deadline approaching (Apr 16)! Don’t miss your chance to join our student-led #TheoreticalBiophysics workshop. Meals, accommodation + reasonable travel covered for accepted participants. Apply ➡️ janelia.news/THB26 @allysonsgro.bsky.social @zamakany.bsky.social
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jmutterer.bsky.social @jmutterer.bsky.social · 01/04/2026
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Pierre-Etienne Fiquet @pfiquet.bsky.social · 31/03/2026
Applications are open for the Junior Theoretical Neuroscientists Workshop which will take place July 21-24, 2026 at the Center for Computational Neuroscience, @flatironinstitute.org Travel, lodging, and meals will be covered for accepted participants. Application deadline: April 15, 2026
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Ahmed El Hady @zamakany.bsky.social · 29/03/2026
Deadline is approaching (April 16th). Send in your applications . All details here: www.janelia.org/you-janelia/... Apply for this workshop at @hhmijanelia.bsky.social intended as a "by the students, for the students" meeting. @janeliaconf.bsky.social
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Leslie B Vosshall PhD @leslievosshall.bsky.social · 28/03/2026
Join us in shaping the future of science! @hhmi-science.bsky.social is hiring a new Scientific Program Officer to support the #HannaGrayFellows #FHScholar programs hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com
Senior Director – Scientific Program Officer
Primary Work Address: 4000 Jones Bridge Road, Chevy Chase, MD, 20815 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute (HHMI) advances the disco...
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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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John Tuthill @tuthill.bsky.social · 24/03/2026
🧵 New preprint led by @bingbrunton.bsky.social, @elliottabe.bsky.social, @lawrencehu.bsky.social We gave a worm brain control of a fly body and it walked What did we learn? Nothing, other than deep reinforcement learning is effective We call it the digital sphinx www.biorxiv.org/content/10.6...
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Stephan Saalfeld @herrsaalfeld.bsky.social · 12/03/2026
Friday, 13:15 (Poster 2-048) at @cosynemeeting.bsky.social #cosyne2026: @allierced.bsky.social and @lappalainenjk.bsky.social present how they made GNNs learn interpretable circuit models from neural activity. Code: saalfeldlab.github.io/flyvis-gnn/
saalfeldlab.github.io
Graph Neural Networks Recover Interpretable Circuit Models from Neural Activity – FlyVis-GNN
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Kim Stachenfeld, PhD @neurokim.bsky.social · 11/03/2026
I have just arrived at @cosynemeeting.bsky.social ! During my flight, as I thought about opening remarks (and had a glass of wine), I got to reflect on why I love neuroscience. Maybe other folks are doing the same and would like to read or add, so I thought I'd do something unusual and share!
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Machine Learning in Science @mackelab.bsky.social · 11/03/2026
@mackelab.bsky.social is at @cosynemeeting.bsky.social #cosyne2026 in Lisbon with two posters presented by PhD students from the lab. Thread below on the projects 👇
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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 · 04/03/2026
Looking forward to heading off to Cosyne next week, and excited to be part of a two day workshop about connectomics, with day one being about species comparison and day two about using data for constraining models. alleninstitute.github.io/connectomics...
alleninstitute.github.io
Workshop – Synapses at Scale - COSYNE 2026
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bioRxivpreprint @biorxivpreprint.bsky.social · 03/03/2026
A central somatotopic map of the fly leg supports spatially targeted grooming www.biorxiv.org/content/10.64898/20…
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Martin Weigert @maweigert.bsky.social · 02/03/2026
Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social
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Nicolas Chiaruttini @nkiaru.bsky.social · 17/10/2024
Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels. #ImageJ #Fiji #BigDataViewer
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Stanley Heinze @stanley-heinze.bsky.social · 01/03/2026
After 5 years of developing, a new preprint from the lab - introducing our workflow for comparative insect connectomics, aimed at democratizing connectomics. @erc.europa.eu @lundvision.bsky.social @biologylu.bsky.social Read it here: www.biorxiv.org/content/10.6...
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