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Stephan Preibisch

@preibischs.bsky.social
1.4K followers 476 following 77 posts

Open Science Software Enthusiast - Director of Scientific Computing Software at HHMI Janelia

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Reposted by Stephan Preibisch
paveltomancak.bsky.social @paveltomancak.bsky.social · 04/09/2025
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
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Sven Dorkenwald @sdorkenw.bsky.social · 15/10/2025
Excited to share more widely: I am starting the Dorkenwald Lab at MIT (McGovern Institute + BCS) in January 2026. We study the organizational principles of neuronal circuits using connectomics. And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
mcgovern.mit.edu
MIT’s McGovern Institute and Department of Brain and Cognitive Sciences welcome new faculty member Sven Dorkenwald - MIT McGovern Institute
The McGovern Institute and the Department of Brain and Cognitive Sciences are pleased to announce the appointment of Sven Dorkenwald as an assistant professor starting in January 2026. A trailblazer i...
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Stephan Preibisch @preibischs.bsky.social · 11/10/2025
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social www.biorxiv.org/content/10.1...
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Misha Ahrens @mishaahrens.bsky.social · 08/09/2025
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...
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Philip Hubbard @philiphubbard.bsky.social · 23/07/2025
What does a neural network look like? Maybe like this view of Larissa Heinrich's U-net for organelle segmentation, with edges between layer inputs and outputs. Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 12/06/2025
🎉 Call for Abstracts! 🎉 We’re celebrating 10 years of #mesoSPIM #opensource initiative – join us at the symposium for talks, demos & posters on open-source light-sheet microscopy, tissue clearing, and imaging! Dates: October 13-15, 2025 Location: Zurich, Switzerland Registration: ema.uzh.ch/R7YRN
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Joshua Weitz @joshuasweitz.bsky.social · 31/05/2025
How bad will it be? Catastrophic. Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come. But, this is the WH's *proposed* budget. Speak up now before it is too late. (inflation adjusted $-s below)
NSF, NASA and NIH budgets per year, inflation adjusted from 2000-2025 along with the proposed cuts. NSF includes research component only. Massive cuts across all sectors, well below support spanning 25 years.
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Stephan Preibisch @preibischs.bsky.social · 27/05/2025
That only took 3.5 months 😅
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Stephan Preibisch @preibischs.bsky.social · 16/05/2025
Looking forward!
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Stephan Preibisch @preibischs.bsky.social · 01/05/2025
Found some pretty cool books at the Marine Biological Laboratory @mblscience.bsky.social library alongside pictures of renowned stylish scientists, with @markkitti.bsky.social, @joshmoore.bsky.social and Graham Johnson. It was overall a very inspiring OME community meeting in Woods Hole!
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GloBIAS @globias.bsky.social · 01/05/2025
#GloBIAS has a blog series - new post out today! Two GloBIAS volunteers reflect on the first version of GloBIAS Free Help (previously Call4Help), explain the idea behind this activity and what was learned during the pilot session. Please check out the webpage: www.globias.org/resources/gl...
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Stephan Preibisch @preibischs.bsky.social · 22/04/2025
The STIM paper is out! We build on established computer vision techniques to automatically create 3D volumes of spatial transcriptomics datasets with human-level accuracy, and useful, interactive visualizations. www.sciencedirect.com/science/arti... @hhmijanelia.bsky.social @mdc-bimsb.bsky.social
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Max Delbrück Center @mdc-berlin.bsky.social · 17/04/2025
Join us in Potsdam for the #HIConference25 by @helmholtzimaging.bsky.social – three days of talks, workshops, community challenges, and some stunning scientific visuals! 🗓 Abstract deadline: May 1, 2025 More info and registration: 🔗 events.hifis.net/event/2061/ #HelmholtzImaging #mdcBerlin
Graphic announcing an event: A purple and orange wave pattern background with symmetrical curved lines creates a visually dynamic effect. A small white "Helmholtz Imaging" logo appears in the bottom right corner. The overlaid text is centered and reads in white, bold sans-serif font: "Helmholtz Imaging Conference 2025. Potsdam, June 25–27. Registration & call for abstracts open."
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Tancredi M Pentimalli @tmpentimalli.bsky.social · 16/04/2025
Our 3D study of the tumor microenvironment is finally out! Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 ) Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!
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Tancredi M Pentimalli @tmpentimalli.bsky.social · 16/04/2025
www.cell.com/cell-systems... CosMx data by @brukerspatial.bsky.social Second harmonics by Andrew Woehler Immunofluorescence by @sonjafritzsche.bsky.social and @josenimo.bsky.social in Fabian Coscia lab STIM for 3D alignment by @preibischs.bsky.social @nukappa.bsky.social et al (coming very soon!)
cell.com
Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment
Pentimalli et al. extend imaging-based spatial transcriptomics to 3D and combine it with ECM profiling. The multimodal analysis of cellular neighborhoods in a clinical lung adenocarcinoma sample revea...
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Stephan Preibisch @preibischs.bsky.social · 05/04/2025
Shout out to my dear #BigStitcher #Windows users :) I finally got access to a Windows VM and fixed many Windows bugs. I hope most functionality is restored. I still advise switching to Linux/Mac, but I will be able to provide more Windows support in the future if necessary.
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Stephan Preibisch @preibischs.bsky.social · 04/04/2025
I recently visited #Amazon HQ2, to present at the AWS Imagine Nonprofit conference 2025. It was exciting to see use cases & opinions from other areas than biomedicine, to make new contacts, and to see how people at AWS work. #AWS has an interesting line up of #conferences & #funding opportunities:
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Kate Miroshnikova @katemiro.bsky.social · 01/04/2025
Check out this new & exciting #postdoc program from Max Planck Society 🤩 - My lab is thrilled to move to MPI MB in Muenster - positions available in #chromatin #mechanobiology #cancer #stemcells #transcription join us!
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NPR @npr.org · 23/03/2025
The Trump administration's erasure of federal data has put the Internet Archive in the spotlight. The organization, with its small but mighty team, is working to help save the world's digital history.
npr.org
Humming along in an old church, the Internet Archive is more relevant than ever
The Trump administration's erasure of federal data has put the Internet Archive in the spotlight. The organization, with its small but mighty team, is working to help save the world's digital history.
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Max Delbrück Center @mdc-berlin.bsky.social · 19/03/2025
🔜 Starting at 5 PM tonight, the @dfg.de will present the 2025 #LeibnizPreis to #mdcBerlin researcher @apombo1.bsky.social and nine other recipients. Congratulations to all of them! 🥳 📺 You can join the action via livestream – click the link below! 👇 #mdcBIMSB | @www.helmholtz.de
youtube.com
👉 LIVESTREAM | Verleihung der Leibniz-Preise 2025 👈
Seien Sie ab 17 Uhr live dabei!
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Stephan Preibisch @preibischs.bsky.social · 12/03/2025
Pretty awesome setting for today’s workshop on enabling access to emerging bioimaging techniques organized by Ian Dobbie at JHU’s downtown DC campus. We had great presentations and discussions; sites.krieger.jhu.edu/iic/workshop...
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Max Delbrück Center @mdc-berlin.bsky.social · 08/03/2025
Happy #InternationalWomensDay ‼️ Over the past weeks, we’ve shared insights from #mdcBerlin's inspiring #WomenInSTEM – highlighting their work, challenges, and career advice. 🔗 Explore all of their stories here: ➡️ www.mdc-berlin.de/about/values... ⬅️ #WomenInScience #mdcDiversity #IWD2025
Graphic with text and colored blocks: Grid-style collage of female scientists in lab coats and professional attire, with "Happy Women's Day!" text in the center, celebrating women in STEM.
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Jean-Yves Tinevez @jytinevez.bsky.social · 01/03/2025
Amazing news on thr #Fiji front. The new launcher holds beautiful promises for better bioimage analysis tools, and not only for Fiji!! See this summary thread by Curtis forum.image.sc/t/fiji-2024-...
forum.image.sc
Fiji 2024 Year in Review: Milestones and Roadmap
Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...
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paveltomancak.bsky.social @paveltomancak.bsky.social · 07/03/2025
Calling the #bioimageanalysis community! Remember the #GatherIsland used during the online #I2K? Remember #Hebedas? #Woodstockbio2025 will be like this, in real life on a #YMCA #campsite in #Czech woods. Bioimage Geeks of the World - Unite and Register! woodstock.img.cas.cz/registration/
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Stephan Preibisch @preibischs.bsky.social · 06/03/2025
Stephan (@herrsaalfeld.bsky.social) of @hhmijanelia.bsky.social explains to the interested Ashburn community how AI can help us understanding biological systems at Old Ox Brewery 😎
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John Skiles Skinner @skiles.blue · 01/03/2025
I got laid off today, with the rest of 18F. 18F was an elite federal software shop. We made gov't websites work better, more efficiently for the American people. We saved taxpayers from getting screwed over by contractors. And were fired for it. We made this website to tell our story: 18f.org
18f.org
We're not done yet | 18F
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Gaia Pigino @gaiapigino.bsky.social · 19/02/2025
“Join the Pigino Lab! We’re hiring a PhD student to explore primary cilia biology using advanced imaging, spatial ‘omics, and AI. Apply now at www.cilia-ai.eu and be part of the Cilia-AI Doctoral Network!”
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Florian Jug @florianjug.bsky.social · 29/01/2025
🚨🚨 MEGA JOB ALERT 🚨🚨 Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social! Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏 More details below... check it out! 🧵 1/3
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Wolfgang Huber @wkhuber.bsky.social · 14/02/2025
Do you love software engineering for exciting biological applications, open science,open source, R, Bioconductor, modern web, cloud& ML technologies? We're looking for a software engineer to work on R/Bioconductor tools for biological data science and AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Picture of the conference centre on the EMBL campus in Heidelberg
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Alper Akay @alperakay.bsky.social · 14/02/2025
Special issue on C. elegans genetics and biology @heredityjournal.bsky.social. Submit your manuscripts by 1st May 2025. Contact me for more info. www.nature.com/collections/...
nature.com
Special Issue: Caenorhabditis elegans genetics and biology
See more information on the new Heredity special issue on Caenorhabditis elegans genetics and biology.
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Teng-Leong Chew @scopeshifu.bsky.social · 13/02/2025
🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.
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Carsen Stringer @computingnature.bsky.social · 12/02/2025
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
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Constantin Pape @cppape.bsky.social · 12/02/2025
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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Lea H. Gregersen @gregersenlab.bsky.social · 13/02/2025
We are recruiting! Center for Gene Expression has 2 or more open positions for PhDs @ucph.bsky.social. Come join our team to work on RNAPII and transcriptional regulation (gregersenlab.com). It's a wonderful city and amazing research environment. Deadline March 6. jobportal.ku.dk/phd/?show=16...
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pm-lab @pm-lab.bsky.social · 07/02/2025
🚨 Job Alert 🚨🔬🧪👩‍💻🖥️ Are you interested in #BioimageAnalysis #ComputerVision #AI #ML methods for the #LifeSciences? Do you want to work on #DigitalPathology of tissues, cells, organelles? Check out this #PostDoc opportunity in a collaboration with Jens Rittscher from @oxengsci.bsky.social @ox.ac.uk
karriere.charite.de
Research assistant / Post-doctoral fellow image analysis - Center for Stroke Research DM.16.25
full-time | 21.02.2025 | Campus Charité Mitte
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Janelia Research Campus @hhmijanelia.bsky.social · 05/02/2025
📢 Submissions are now open for the CellMap Segmentation Challenge. Build the best method for segmenting cellular organelles in vEM using our 289 annotated volumes, 40 organelle classes, and 22 diverse cell and tissue types. 🔗 hhmi.news/410evJQ
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Eric Topol @erictopol.bsky.social · 24/01/2025
Welcome immigrants from X interested in science to the friendlier skies of @bsky.app, as documented by a new @nature.com survey (but you already knew that 😉) "Bluesky is much better for science. There is much less toxicity, misinformation, and distractions." www.nature.com/articles/d41...
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Stephan Preibisch @preibischs.bsky.social · 21/01/2025
I wonder …
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Stephan Preibisch @preibischs.bsky.social · 19/01/2025
Very excited to read this: The nature of the last universal common ancestor and its impact on the early Earth system www.nature.com/articles/s41...
nature.com
The nature of the last universal common ancestor and its impact on the early Earth system - Nature Ecology & Evolution
Integration of phylogenetics, comparative genomics and palaeobiological approaches suggests that the last universal common ancestor lived about 4.2 billion years ago and was a complex prokaryote-grade...
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Aafke Gros @aafkegros.bsky.social · 15/01/2025
Microscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1...
FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023
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BWJones @bwjones.bsky.social · 11/01/2025
Now for my Max Planck peeps… Get yer institutions onto Bsky and off of X.
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Nicolas Chiaruttini @nkiaru.bsky.social · 11/01/2025
Finally had a bit of time to play with multi-GPU deconvolution. Using @truenorth-ia.bsky.social and @haesleinhuepf.bsky.social previous work. Here it is in action in #BigDataViewer using async and lazy processing. Look at the two poor laptop GPUs going as fast as they can:
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Stephan Preibisch @preibischs.bsky.social · 07/01/2025
It seema a bit weird that @fairfaxcounty.bsky.social public schools are still closed on Wednesday. Why? Streets are completely free, no new snow …
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Rita Strack @ritastrack.bsky.social · 06/01/2025
@glaevsky.bsky.social is LSFM a conference and training course again this year? I'd like to come if there's a conference portion!
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Stephan Preibisch @preibischs.bsky.social · 22/12/2024
I was very impressed with the great food at the Green Kitchen Lab at the Irchel campus of the Zurich university: “The culinary offering is based primarily on seasonal, regional and, as far as possible, natural food from plant sources.” www.mensa.uzh.ch/en/menueplae...
mensa.uzh.ch
Green Kitchen Lab
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Janelia Research Campus @hhmijanelia.bsky.social · 16/12/2024
We’re #hiring Theory Fellows. 🥼 Our Computation & Theory research area is recruiting early-career scientists to test theories, collaborate across research areas & tackle fundamental questions in biology. Apply by Jan. 7 ➡️ janelia.link/theoryfellow... #computationalbiology
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Stephan Preibisch @preibischs.bsky.social · 16/12/2024
Winter is coming in Leesburg near @hhmijanelia.bsky.social
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Erick Ratamero @erickratamero.com · 13/12/2024
This is a dream job position for a small but not insignificant portion of you, probably!
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Stephan Preibisch @preibischs.bsky.social · 13/12/2024
We have to go buy toilet paper, the aliens are coming!!! This will be worse than Covid …
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