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...

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...

🎉 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

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)

That only took 3.5 months 😅

Looking forward!

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!

#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...

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

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/ #HIConference25#HelmholtzImaging #mdcBerlin

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!

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!)

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.

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:

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!

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.

🔜 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

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...

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...#InternationalWomensDay⬅️ #WomenInScience #mdcDiversity #IWD2025

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-...

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/

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 😎

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

“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!”

🚨🚨 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

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...

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/...

🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.

#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...

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...

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...

🚨 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

📢 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

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...

I wonder …

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...

De novo designed proteins neutralize lethal snake venom toxins | Nature www.nature.com/articles/s41...

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...

Now for my Max Planck peeps… Get yer institutions onto Bsky and off of X.

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:

It seema a bit weird that @fairfaxcounty.bsky.social public schools are still closed on Wednesday. Why? Streets are completely free, no new snow …

@glaevsky.bsky.social is LSFM a conference and training course again this year? I'd like to come if there's a conference portion!

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...

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

Winter is coming in Leesburg near @hhmijanelia.bsky.social

This is a dream job position for a small but not insignificant portion of you, probably!

We have to go buy toilet paper, the aliens are coming!!! This will be worse than Covid …

Congratulations Ana, this is amazing!

Fenestrae are unusual holes in hepatic endothelia cells. Here they are in a data set from OpenOrganelle, reconstructed by Aubrey Weigel and the CellMap team at #HHMIJanelia. This video was rendered in #Blender driven by neuVid (which has been helpful for #CellBiology as well as #Neuroscience).

Winter sunsets are the best. Did I mention that the Champalimaud PhD program just opened for applications and that the lab has an open postdoc position in metabolism?