Stefan Dvoretskii, Anwai Archit, Constantin Pape, Josh Moore, Marco Nolden: BioimageAIpub: a toolbox for AI-ready bioimaging data publishing https://arxiv.org/abs/2512.15820 https://arxiv.org/pdf/2512.15820 https://arxiv.org/html/2512.15820

#NFDI4BIOIMAGEfromAtoZ - P as in Pixels. In biological microscopy, #pixels are more than just image dots – they are quantitative measurements that encode spatial and intensity information at the core of high-dimensional bioimaging data.

🚨 PhD Position Available 🚨 I’m recruiting a PhD student to join my lab at the Multiscale Imaging Centre (MIC), Münster, Germany. www.bischofflab.com/jobs Fully funded ✅ #Cellbio #Morphogenesis #Microscopy #Drosophila #PhD (Details Below) Original Posting: stellen.uni-muenster.de/jobposting/d...

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:

Can we please discuss accessibility at conferences? When organizers and schedules assume that everyone can walk fast and climb stairs, people with mobility issues (visible or invisible) might feel excluded. /

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io

Hopping on the ✨ 🚅 to Dresden after a week of #OME_NGFF_Hackathon. Looking forward till next time 😃

We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.

Happy Hackers @ #OME_NGFF_Hackathon

This is what hacking *actually* looks like. #OME_NGFF_Hackathon

OME-NGFF Hackathon in Zürich just started! We're organizing ourselves to dig into various topics during the next few days. Let's shape the future of microscopy image data standards together. #OME-NGFF_Hackathon #GerBI

Co-organized by @nfdi4bioimage.bsky.social through @joshmoore.bsky.social & Christian Tischer, we're happy to see the #OME_NGFF_Hackathon 2024 in full swing! Exciting work bringing forward #OMEZarr for #FAIR bioimage data management. Shout out to the host BioVisionCenter! @gerbi.bsky.social #NFDI

Job alert! We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? See also on the forum: forum.image.sc/t/research-e...

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 🧵)

🚀 Registration is open for BioHackathon Germany 2025! Join us 1–5 Dec in Walsrode for hands-on projects, networking, and innovation in #bioinformatics. 🧬🤝 🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel 🔗 Seats limited—register now! www.denbi.de/de-nbi-event... #Hackathon

So it seems like #LinkedIn also wants to start using your personal data to train #AI models 🙄 Opt-out here: www.linkedin.com/mypreference...

The new Thermal Trace app from #C3S and #ECMWF is here! 80+ years of thermal stress data based on “feels-like” temperatures for any location worldwide, now at your fingertips. Fast, intuitive, interactive – and free! Read our article for the full details and head to the app. 🔗 bit.ly/46ZMllL

Whenever I feel down, I have a 👀 at the download statistics of that #opensource data-repository I and my team at OncoRay (Dresden) compiled during my PhD at @tudresden.bsky.social @hzdr.bsky.social. 😌 rodare.hzdr.de/record/3131

🎉 Amazing NEWS for #ImageAnalysis & #LifeSciences folks! The ultimate #imageanalysis #hattrick is here 🧠🔬✨ www.biovoxxel.de/individual-w... Read the 🧵👇 All necessary info and links at the end ! #bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning

Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...

Suitable @poldresden.bsky.social farewell cake for a #bioimage analyst? 🥮🤤

Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)! More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥

As good as a time as any to announce: After a great time at @poldresden.bsky.social I'm looking forward to starting my new position at @gerbi-gmb.de as a software developer for @openmicroscopy.org 🔬😀! Scalable #RDM solutions in the ome-zarr-verse, here we come!

#EUProject | #BioImaging & AI ➡️ BioImage Model Zoo by @ai4life.bsky.social is a platform for #AI models in biological imaging ➡️ To find out about the training courses and tools available to help you use the platform correctly for your area of study, visit: www.embrc.eu/project/ai4life/ 🌊🧪🦑

Zarr is hiring again! Build scalable bioimaging solutions, collaborate globally, and join the Friedrich Miescher Institute for Biomedical Research as a Computational Scientist or Research Software Engineer www.fmi.ch/education-ca...

#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis @mazoc.bsky.social

Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.

Reminder: Last chance to join our Helmholtz OMERO workshop! Learn to organize & annotate your bioimaging data with Fiji, Python & more. 📅 July 17 | Online | 25 seats Register by July 7 👉 https://events.hifis.net/event/2734/ #HelmholtzImaging #HIFIS […] [Original post on helmholtz.social]

Check out our latest release of the napari-clusters-plotter plugin! It is so versatile now, try it out with your data! @jo-soltwedel.bsky.social did a great job refactoring a lot of the code to ease its maintainance! ⚙️🔧

@stadt-dresden.bsky.social covered in smoke from earby wildfires. So this really is the new normal, huh...😒 #climatechange

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 👇🧪💻🔬

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...

New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇 First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:

Wait, wait, wait....v0.6.0 is just out, but there is already a next big feature coming to napari? Yes! You see it right 😊 (more impressive demo coming soon) . Our own @brisvag has been doing work on multichannel grid mode which is to replace our current grid […] [Original post on fosstodon.org]

That's cool: For a brief amount of time yesterday on May 1st, #solarpower accounted for the entire entire demand of the German grid - and more! Makes me happy to contribute with my measly 800W on my balcony 😅

I quite like this design - I find it easy to compare left and right arch, and the message is about that. Not the absolute quantities over the years. ❤️ 🏳️‍🌈

Take a gander at those young faces! www.openmicroscopy.org/teams/ has been updated with the GerBI #OME team's (slightly dated) looks 📸👀 Thrilled to continue contributing to #FAIR data infrastructure @openmicroscopy.org as a part of the @dfg.de funded @nfdi4bioimage.bsky.social and #i3dbio projects!

Thanks to Hanjin Liu, napari now has a command palette! 🎨 This thing is really nice to use — the core team can no longer live without it — and it even works with plugin commands! 🤩

Some new additions for the upcoming @napari.org clusters-plotter version 👉0.9.0 around the corner! Powered by some work from @mazoc.bsky.social, it casually turns into a pretty neat tool for feature map creation 😀 github.com/BiAPoL/napar...

Biggest commitment to a 3 second joke I've ever seen

#Hanami in @stadt-dresden.bsky.social 😃

Only five days remain to register!* Here is the tentative program: *: it is likely that there won't be a deadline extension.

👏 #TiM2025 is successfully wrapped up! A huge thank you to the entire organizing team, especially our managing director @janinahanne.bsky.social and our project manager Klara Diester, for their weeks of dedication and planning. We were thrilled to make this amazing event possible! 🙌

Takeaway after the workflow session at #TiM2025: I'll make all my processing functions command-line-executable so I can simply hook them into @nextflow.io. Would be cool if @napari.org plugins supported this natively for function GUIs!

Learning about image segmentation tools in napari/python with @jo-soltwedel.bsky.social & @zoca-biodev.bsky.social at the #TiM2025. Excellent Workshops and great people here in Münsingen. 🎓🧑‍🔬 #gerbi-gmb

2hrs into #TiM2025 and already mind=🤯. Rendering entire animals and human organoids in 3D and observing organism-wide disease distributions by @erturklab.bsky.social

📣Just released napari-omero 0.4.0📣 Bug fixes, better metadata handling and overall smoother integration with @openmicroscopy.org standards. Thanks to @psobolewskiphd.bsky.social for all the valuable contributions! And more in the making...☺️ --> github.com/tlambert03/n...

Fancy new #3dprinting toy 🤩 Maybe I'll start printing all my collaborators some of their data for segmentation tasks as giveaways 🤗