Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊 Huge kudos to Max Hess for this PhD milestone! 💪 @lucaspelkmans.bsky.social shorturl.at/cO0u7 Let's zoom in!

The #mesoSPIM symposium really opened my eyes to the power of open source hardware. I've highlighted some of the surprising outcomes in a new blog post: How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium www.syglass.io/blog/how-ope...

Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!

We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...

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...

🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️ jobs.helsinki.fi/job/Helsinki... #jobopening

Job opportunity at the University of Zurich! 📢 We are looking for a 𝐋𝐚𝐛𝐨𝐫𝐚𝐭𝐨𝐫𝐲 𝐓𝐞𝐜𝐡𝐧𝐢𝐜𝐢𝐚𝐧 / 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐀𝐬𝐬𝐢𝐬𝐭𝐚𝐧𝐭 (𝟒𝟎%) to join our Microscopy Innovation Platform (MIP), an open-source initiative focused on advancing and making light-sheet and multiphoton microscopy accessible to researchers. 1/3

@nfdi4bioimage.bsky.social Task Area Leaders Josh Moore and Christian Tischer will introduce participants to the history and basics of OME-Zarr at the international 2025 OME-NGFF Symposium from November 10–11 in Zurich, SW. Register here: 👉 www.ema.uzh.ch/de/register/... Picture by BioVisionCenter

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 looking for an enthusiastic postdoc to join our team. 😊 The project focuses on protein design and cryo-EM applied to cancer research. 🔬🧪 The position is fully funded for 3 years. Please share 🙏 Job description and application details (deadline: October 11th): www.cnio.es/en/empleo/po...

napari 0.6.5 is out! 🚀 Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: napari.org/dev/release/...

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

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)

Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...

Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org @tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev

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)

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊 📄 joss.theoj.org/papers/10.2110… (1/3)

Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden Wednesday, 27th of August, 2pm CEST

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!

I'll be there! Giving a talk! and hacking on _something_ for a few days!

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 🧵)

Huge congratulations to Clara Baader on successfully defending her PhD this week! Her research explored how mechanical forces and biochemical signals coordinate to guide intestinal development and repair 🎓

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!!! 🔥🔥🔥

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...

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!

And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be: www.youtube.com/watch?v=8t8R...

Are you looking for a postdoc? I will be looking for 2-4 people after the summer to join the lab !! Do not hesitate to reach out and disseminate !!

🌐 Junior Web Developer / Scientific Prototyper 🛠️ Job Alert: Web Developer / Scientific Prototyper (up to 100%, fully remote, based in EU) We’re looking for a creative web developer to build engaging tools and interactive demos for the imaging community.

🧠 Metadata and Standards Lead 🛠️ Job Alert: Metadata and Standards Lead (up to 100%, fully remote, based in EU) We’re looking for a thoughtful and technically skilled expert to help us shape the future of metadata in bioimaging.

🚨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...

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

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

🚀 We just released a major Fractal update! More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr. Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...

🚨 Last chance to register for the BioImage Informatics Finland Network Symposium! 📍 Seili, Turku archipelago 🇫🇮 🗓️ 22-23 May 2025 ▶️ Open for international participants ⏳ Register by 25 April 2025 ⤵️ crm.abo.fi/Events/4511/... 🔗 program and more info: www.bioimaging.fi/biif2025/ #BIIF2025

🌟 Exciting News! The program for the BioImage Informatics Finland Network Symposium is out ⤵️ bioimaging.fi/biif2025/ ⛵️Check out the program and and join us at Seili island, Finland on May 22-23, 2025 ⌛️Register by April 25: crm.abo.fi/Events/4511/... #BIIF2025

First preprint from my PhD is now online! We show that deep learning can recognise modes of action of antibiotics directly from brightfield images of bacteria. 🦠

I'm amazed anyone thinks LLMs are fit for medical applications. I asked ChatGPT "How many cells are in this image?" and gave it three different images of exactly the same sample. It will be obvious to an experienced image analyst what's gone wrong here, but probably not to a typical life scientist.

ICYMI: A MATLAB implementation of @zarr.dev has dropped from @mathworks.bsky.social 🚀 github.com/mathworks/MA...

‪ #OME-Zarr just got a boost! 🚀 The OME-NGFF #Hackathon in Zurich, organized by the BioVisionCenter UZH & co-organized by @nfdi4bioimage.bsky.social, significantly advanced OME-Zarr, the cloud-native file format for large bioimaging data! ➡️ Find the hackathon report here: osf.io/5uhwz_v1

Turns out that when a group of interesting and enthusiastic scientists who care about open standards sit together for a couple of days, they do great things 🔥🔥🔥

Do you want to learn #BioimageAnalysis? Do you want to strengthen your skills? We're thrilled to announce the #NEUBIAS Pasteur Course on Bioimage Analysis - May 2025! in @pasteur.fr Paris! research.pasteur.fr/en/course/ne... Details are on the page linked here, some info below 👇

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀 Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich. 🔗 Read the preprint: osf.io/preprints/bi... 🧵 (1/15)

We're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!

🚨Job alert: We're hiring a Data Scientist (Image Analysis) to join our Facility for Advanced Imaging & Microscopy. The facility provides cutting-edge light and electron microscopy, high-content screening, image analysis and spatial-transcriptomics services. Apply at: www.fmi.ch/education-ca...

Hi folks! napari is officially on bsky now! 🥳 Let's hit the ground running with a reminder that all are welcome at our next (Atlantic) community meeting on Feb 12, 8:30am SFO / 11:30am NYC / 5:30pm Paris. Agenda and details here: hackmd.io/BXWDZ3i8Q6OA...

We're hiring! Our IT Team is looking for a Linux Systems Engineer to support scientific computing and big data management. Apply here: www.fmi.ch/education-ca...

TL;DR installers are really challenging to make. The team made some tooling for @napari.fosstodon.org.ap.brid.gy that was so fantastic that it is spreading across the scientific python ecosystem!

We are searching for a highly motivated and talented computational postdoc with an interest in translational spatial omics to join our team in Heidelberg. Apply now! karriere.klinikum.uni-heidelberg.de/index.php?ac...