Been a while since I did this so I'm behind, but here's another batch of tools (somewhat) fresh from the bioRxiv)

One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇

Looks like someone is misusing GloBIAS and its president name to approach people for money transfers. Please note - GloBIAS will always send proper payment requests and has no need for members and volunteers to transfer money on their behalf.

Our November issue is now live! 🎉 www.nature.com/nmeth/volume... On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...

Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)

Felix Zhou's u-Segment3D is out: www.nature.com/articles/s41... It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation. It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.

🚀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 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...

Great to see Node staff, #i4A training grantee hernanmn.bsky.social & others at the EMBO "Advanced Methods in BioImage Analysis" course! @ahklemm.bsky.social @perrinegil.bsky.social @jytinevez.bsky.social @france-bioimaging.bsky.social @iemcas.bsky.social More🔽 www.eurobioimaging.eu/news/success...

Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones. If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.

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.

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

Let's finish the day with the round table discussion 🗣️💬 fantastically led by @ahklemm.bsky.social and Suganya Sivagurunathan from @scilifelab.se & Uppsala University! So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩‍💻 in image facility projects 🔬

What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜

🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮 www.scilifelab.se/news/ready-t...

Better ML for cryo-ET starts with better benchmarks. We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge. The result: community models beat expert tools. Read more in the @natmethods.nature.com article that just came out: 🔗 doi.org/10.1038/s415...

Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects! My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally. Check out my portfolio and contact: acorbat.github.io

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!

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

The #CBIAS2025 abstract deadline is this Sunday, August 31st. Submit your #BioImageAnalysis work, whether it’s a new tool or a biological discovery. #EarlyCareerResearchers, this is for you! Short and flash talk slots are up for grabs. www.crick.ac.uk/whats-on/cri...

I am stunned! First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers. If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE on LinkedIn buff.ly/cLPh8eZ #bioimageanalysis #biovoxxel #fiji

A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3) forum.image.sc/t/qupath-ext...

My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess. Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩 scads.github.io/embo-lsm-bia...

New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).

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!!! 🔥🔥🔥

Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):

Day 2 of #Zidas2025 is happening! After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !

Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths". More in our preprint: www.biorxiv.org/content/10.1...

New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis - paper: elifesciences.org/articles/99848 news: tinyurl.com/y2hpmbb9

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

Deadline approaching tomorrow!

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.

So much looking forward to this! 🤩 We're thrilled to be running a new instance of our "Advanced Methods in Bioimage Analysis" course. It's going to be a blast! Apply by June 4th.

Ready to step into bioimage analysis in Python? The course mastermind 🧠 has just launched a new course:

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...

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

🌌 Missed the presentation on “Image Analysis Using Galaxy” by Beatriz Serrano-Solano, Leonid Kostrykin, Anne Fouilloux and Riccardo Massei as part of the #GloBIAS Seminar Series? Watch it now on the GloBIAS YouTube channel: www.youtube.com/watch?v=wAHO... To the slides: zenodo.org/records/1494...

End-of-week news! The selected projects for the 3rd AI4Life Open Call are here: 🔹 Phase 1: Consultation – 10 projects received expert guidance 🔹 Phase 2: Deep Learning Support – 8 projects selected for in-depth AI-driven bioimage analysis 🔍 More at: ai4life.eurobioimaging.eu/third-ai4lif...

Lemmings (1991)

“We love #microscopy and thanks to the infrastructures at SciLifeLab we can develop new methods and establish original views on human #CellBiology” says Bennie Lemmens (SciLifeLab & @ki.se) 🧪 Image: #SuperResolutionMicroscopy image of replicating human epithelial cell with two nascent #DNA labels

Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.

🚨 Save the Date! 🚨 AI4Life & @globias.bsky.social are hosting a 4-part webinar series to showcase AI4Life services and lessons learned. 📅 When: Feb 13, Apr 10, Jun 12, Aug 14 🖥️ How: Online | 🎥 Recorded 🔗 Registration: bit.ly/registration...

Info for my fellow German Expats. If you are not registered in Germany anymore, you might find this information useful for how to vote. The form has to arrive at the municipality you last lived in by Feb 2. You can send it - new feature - by e-mail. www.bundeswahlleiterin.de/bundestagswa...

New paper out! We share our experiences from conducting #bioimageanalysis workshops, using open-source software and building a community around training: doi.org/10.1002/jemt... Thanks to the dream team of rockstars, @david-j-barry.bsky.social, @martinjones.bsky.social and Tom Slater

Not only that, but the posters from #CBIAS2024 are now online! crick.figshare.com/collections/...

Imaging Friends, we just published our #CBIAS2024 conference recap, featuring impressions from @dgaboriau.bsky.social and @fmlove.bsky.social. If you want to know how amazing this edition was and get hyped for the next one, check our blog post on @focalplane.bsky.social

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

Necesitas ayuda con analisis de imagenes, desde @globias.bsky.social vamos a ofrecer sesiones de Call4Help. En la encuesta podes llenar si necesitas que la sesion sea en otro idioma y que herramienta preferis (Napari, Ilastik, Fiji, CellProfiler, etc). docs.google.com/forms/d/e/1F...

Why #BigDataViewer loves multi-resolution (pyramidal) formats: - Top left: Only high-res data → slow & artifacts when zoomed out. - Top right: Only low-res data → no details when zoomed in. - Bottom: All resolutions → seamless, responsive, beautiful. 🎥 #FijiSc

Recurring analysis requests leading to tools that should be as generalisable as possible and therefore usable by multiple user groups on their specific data. #CBIAS2024