Anna Klemm

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!!! 🔥🔥🔥

GloBIAS: strengthening the foundations of BioImage Analysis There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...

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

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 !

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...

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...

Self-supervised, label-free 3D cell imaging is here EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...

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

F-BIAS: Towards a distributed national core facility for bioimage analysis † Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...

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:

Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.

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...

Ask Erin, Dear Beth On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...

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)

YouTube video by GloBIAS Image Analysis using Galaxy by B. Serrano-Solano, A. Fouilloux, L. Kostrykin, R. Massei

🌌 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)

The image shows a microscopy image of a replicating human epithelial cell with two different nascent DNA labels in cyan and magenta, which was imaged with super resolution microscopy (3D-SIM) at the SciLifeLab Advanced Light Microscopy unit.

“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...

Enhancing Research Through Image Analysis Workshops: Experiences and Best Practices This graphical abstract illustrates the structure of interactive image analysis workshops, where participants engage in hands-on learning with open-source tools under expert guidance to improve resea...

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/...

Crick BioImage analysis Symposium (CBIAS2024) Overview of the 2024 edition of the Crick BioImage Analysis Symposium featuring impressions from 3 microscopists

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

Method of the Year 2024: spatial proteomics - Nature Methods Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.

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...

GloBIAS Call4Help: Session Feedback and Preferences Come and get your image analysis questions answered! GloBIAS (globias.org) is organizing virtual community sessions where you can sign up for a time slot to work one-on-one with bioimage analysis expe...

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

Spatially clustering with @acorbat.bsky.social for the Crick BioImage Analysis Symposium #CBIAS2024

Thanks @simonfn.bsky.social for sharing and for the invite to the Bluesky!👋

And yes, we have a job opening - come work with us @ www.scilifelab.se/units/bioima... ! 💻🔬🦠

Details on forum.image.sc/t/bioinforma...