Back to work on #bigvolumebrowser, I've added the import of point clouds that change over time. The test data generation was a pleasant detour into the world of attractors (Thomas' cyclically symmetric is shown).

Hi Fans of Smart Microscopy, Are you ready to automate your next large scale microscopy experiment and work smarter, not harder? Join us for the Smart Microscopy workshop organized by EPFL Bio-Imaging Platform (Lausanne) and @zeiss-microscopy.bsky.social www.zeiss.ch/mikroskopie/...

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)

You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!

Are you working with OME-Zarrs in Switzerland? We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)

🔬 Free microscopes + teacher training! 📅 Applications are now open. To apply, visit www.foldscope.com or scan the QR code (video) ✉️ Any questions? Email us at [email protected] #stem #education #science #teachers #training #free #microscopy #educators #professionaldevelopment #microscope

Reconstructing long-range axons from dense brain images is tough. This study introduces a novel method that separates axon identification from global statistical rules, showing big improvements over existing tools for mapping neuronal projections. buff.ly/o7QmH4B

Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)? Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.

Join EMBL AI! We have ambitious plans to transform life sciences research through AI. Interested in using ML/AI to solve complex interdisciplinary challenges? We’re looking for two senior leaders based at EMBL Heidelberg👇

Check out the PyCon Au talk from my team member: @ishratz25.bsky.social on the challenges and solutions(?) of cell counting in whole-brain light sheet images! Also give her a follow, she's new here. www.youtube.com/watch?v=ccLn...

Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030 abo.rekrytointi.com/paikat/index...

Want to enhance your image analysis skills with napari? We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data. 🕒 Applications close on 15 September. Learn more and apply 👇 www.crick.ac.uk/whats-on/cbi...

New @maxplanck.de study: We looked for left-right differences of gene expression and cell-type abundances in the brains of MICE 🐭using Xenium @10xgenomics.bsky.social. Possible clues to how functional brain asymmetry is supported !! www.biorxiv.org/content/10.1... Short thread below ⬇️

Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇

Reconstructing long-range axons from dense brain images is tough. This study introduces a novel method that separates axon identification from global statistical rules, showing big improvements over existing tools for mapping neuronal projections. buff.ly/OBKr9cM

📢 Recruitment for the EMBL International PhD Programme is officially open! At EMBL, we train young scientists to become skilled and creative future leaders in academia and other sectors. Join us and get a head start on your career in life sciences! bit.ly/47mmiFF

Interested in data management in microscopy not only in the light but also in the electron (microscopy) world? Chat with Conni Wetzker at the shared booth (No. 57) of @nfdi4bioimage.bsky.social, @fairmat.bsky.social and MatWerk at the #MC2025 in Karlsruhe. To our poster: zenodo.org/records/1701...

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...

Hello! Very excited to share our latest preprint, which is great news for us but terrible news for any diehard fans of PSNR and SSIM as image quality metrics in microscopy... (1/5) www.biorxiv.org/content/10.1...

Are you ready to develop your bioinformatics skills? From #AlphaFold to microscopy data analysis, make 2026 the year you develop your knowledge with @training.ebi.embl.org and @events.embl.org. 👉 View the calendar: embl.org/about/info/c... #datascience #computationalbiology #lifescience 🧬🖥️

Have a research project that requires analysing microscopy data? Master the skills you need in our upcoming ‘Introduction to image analysis’ technical training course. 📅 27-28 October 📍 The Francis Crick Institute For more info and to apply 👇 www.crick.ac.uk/whats-on/int...

if you're a teacher who wants to bring science to life in the classroom, @skypeascientist.bsky.social brings scientists to your class. Sign up at: www.skypeascientist.com

one small consolation of being a 60+ year old investigator is the ability to submit to 𝘔𝘈𝘛𝘜𝘙𝘌 family journals — sure they’re low impact (for our knees) but they have an early bird special if you submit between 4:00 and 5:30 on weekdays

Would your #cellbio research benefit from you attending a #Microscopy or #BioimageAnalysis training course? For grants of up to £1,000, check out our Microscopy Training Grants with @focalplane.bsky.social Next deadline: 5 September 2025 www.biologists.com/grants/jcs-f...

@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software. Learn more: youtu.be/0g_MkTa_NwQ #EurekaPrizes

18 If you’re interested in the videos or the brain surface poster, you can find them here zenodo.org/records/1603... and zenodo.org/records/1596... Also, if you have a species we don’t yet have, say hi :D 🥰

1 To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised! 🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...

Multiscale characterization of myelin distribution with polarized THG microscopy Morizet et al, Optica 2025 doi.org/10.1364/OPTI... @laboptbio.bsky.social @institutducerveau.bsky.social @cnrs.fr ‪‪ @ip-paris.bsky.social @inserm.fr (1/8)

Submit your method to our denoising challenge!!! 👍

🚀 We’re hiring again! Join @gerbi-gmb.de as a Software Developer! 💻 Build scalable #bioimaging solutions 🌍 Collaborate globally 🎯 Contribute to open science through #OME #Zarr 📣 Tell your #NGFF friends. Remote, full-time. Apply by 30 June 2025: All submissions via bit.ly/gerbi-jobs-2...

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging Let's have a look 👇🧪💻🔬

Congratulations to @caporalclement.bsky.social on his brilliant defence of his PhD thesis, entitled 'Quantitative Analysis of Large Volume Imaging in Developmental Neurobiology' !

🚨We're hiring! Join a global team at the @priscaliberali.bsky.social lab & the @alleninstitute.org to build cutting-edge image analysis workflows for complex biological datasets, including light-sheet microscopy images. Apply at: www.fmi.ch/education-ca...

Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology! 🎉✌️ journals.plos.org/ploscompbiol... So happy about this paper and how the work turned out. A small thread 👇 #bioimageanalysis #corefacility

Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST! Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...

🚨 We’re hiring TWO new colleagues! 🧠 Structured Metadata Expert – Design data models, standards & annotations for #OMEZarr 🌐 Web Developer / Prototyper – Build interactive tools & demos for the community Both fully remote. Both open science. 🔗 gerbi-gmb.de/resources/ca... #RSE #OpenScience

(almost) every talk from OME 2025 is now on YouTube! If you care about microscopy data and about open-source, you should definitely check them out. www.youtube.com/playlist?lis...

Any scikit-image fans in Vienna? The skimage team would like to meet in Vienna for a code sprint Aug 14-16 ahead of EuroSciPy. We'd super appreciate it if someone's workplace can host us! All we need is electricity, natural light, and (most important) walking distance to coffee. ☕️😂🙏

We've extended the deadline to May 21st - you now have 1 WEEK LEFT to come hang out with us in Boston and learn to think like bioimage analysts. We'll have a lot of fun!

Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social

💻 Apply to our beginner-friendly Boston Bioimage Analysis Course! Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required! Fee waivers available thanks to funding from @bioimagingna.bsky.social! 🗓️ Apply June 1st! iac.hms.harvard.edu/bobiac/2025/

Second round of hashtag#GloBIAS Free Help (previously Call4Help) is happening in May. You can register for the sessions on our webpage: www.globias.org/activities/g... Registration deadline is 7. May 2025.

BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...

Please check out BiaPy from Muñoz-Barrutia, Arganda-Carreras, and colleagues for user-friendly deployment of deep learning tools for bioimage analysis. www.nature.com/articles/s41...

Finally BiaPy is out in Nature Methods! 🥳🥳🥳 A major milestone in my research! I'm incredibly proud of the progress made. Huge thanks to my PhD supervisors, @iarganda.bsky.social and @arratemunoz.bsky.social , for their invaluable guidance and support throughout this journey. Check out the thread🧵👇

🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy

If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2) forms.gle/C8dUpg8qZkbD... #bioimaging #microscopy #bioimageanalysis

My first preprint is out! "DINOSim: Zero-Shot Object Detection and Semantic Segmentation on Electron Microscopy Images" 🔬✨ 🔗: doi.org/10.1101/2025...