I just published a critical bugfix to bia-bob, the AI coding assistant within Jupyter. Updating code within cells should work again! Try it out: pip install bia-bob==0.36.2 github.com/haesleinhuep...

Helmholtz Imaging Conference 2026: abstract submissions deadline extended! Submit your contribution by 30/9 👉 events.hifis.net/event/3981/p... Inspiring keynotes, new formats, workshops, community spirit & Kunstkraftwerk Leipzig await! See you there! 👋 @helmholtz.de @helmholtzai.bsky.social

Proud to present the publication of napari-lattice – our solution to the immense computational requirements of Lattice Light Sheet and Oblique Plane Microscopy. onlinelibrary.wiley.com/doi/10.1111/... Before I get into the thread, the important part is on github: github.com/BioimageAnal... (1/n)

napari‐lattice: A user‐friendly image processing tool for lattice light‐sheet microscopy data

Lattice light-sheet microscopy (LLSM) enables researchers to capture high-speed 3D videos of living cells with high definition and minimal damage. However, this technology generates terabytes of data....

onlinelibrary.wiley.com

Just for the record: That's my first week @scadsai.bsky.social Dresden/Leipzig where I work more in Dresden than in Leipzig 😅

This week, @mpi-cbg.de celebrated its 25th anniversary. 🎂 @haesleinhuepf.bsky.social, @scadsai.bsky.social researcher and an alumnus of the MPI-CBG, gave a talk at the anniversary symposium about "How Generative AI impacts [BioImage] Data Science". Find his slides here: 👉 doi.org/10.5281/zeno...

My slides about "How Generative AI impacts [BioImage] Data Science" I presented @mpi-cbg.de yesterday are #openaccess Big thanks for having me! I was a pleasure to be back for the 25th Anniversary of MPI-CBG! doi.org/10.5281/zeno...

I guess M.C. Escher would endorse the arrows in this schematic drawn by Gemini 🤯

Challenge of the day: Use free AI credits before midnight. 😅

The most recent #biabob release brings support for AI-generating multiple code cells within your Jupyter Notebook. Works great with claude-sonnet-5, gpt-5.6-luna and JupyterLab 4.6. github.com/haesleinhuep...

I just automated reviewer3. It provides feedback on .docx manuscipts, per default privacy preserving through local LLMs, friendly, professional and constructive. Great if you need quick feedback and suggestions within a document and all colleagues are on vacation. 📃 👁️ ✏️ 🚀 github.com/haesleinhuep...

Blast from the past! Did you know you can create clean, readable notebooks for the ImageJ Macro language? A great way to build tutorials, teaching materials, and [mentally] reproducible image analysis workflows. 👨‍🏫📜🚀 github.com/haesleinhuep...

Last Tuesday, @sweidtkamp.bsky.social, @schmchris.bsky.social, @joshmoore.bsky.social, @antjekeppler.bsky.social and @haesleinhuepf.bsky.social represented @nfdi4bioimage.bsky.social at the @nfdi.de interim report symposium, reporting on the consortium's progress and activities within the community.

Cast yourself as a villain

Not Listening Office Space

ALT: Not Listening Office Space

static.klipy.com

Christophe 🔬 Leterrier@christlet.bsky.social · 3mo ago

Cast yourself as a villain

No live nuclear label? No problem. Use artificial labelling to infer DAPI-like nuclei, then use #NucleiSky to align your data. For instance, to connect live imaging data to fixed Cell Painting images.

Guillaume Jacquemet@guijacquemet.bsky.social · 3mo ago

Delighted to share our latest preprint "NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations" www.biorxiv.org/content/10.6... Code and App: github.com/CellMigratio...

Try out Vision-Embedding-Space-Travelling in your browser with one click 🦋🚀 livinglab.scadsai.uni-leipzig.de/vest/ Thanks to our @scadsai.bsky.social Living-Lab team for deploying it 🤩 If you want to try it with your own data, check out documentation and #opensource code: github.com/scads/vest

Just playing with #StrixHalo, the new APU from AMD built into a 13inch laptop. Loading a 31b model takes 5 minutes, but then the performance seems amazing for local LLM inference!

#NewProfilePic

Want to build some of the most advanced light-sheet microscopes in the world to watch life assemble itself cell by cell? The Royer Lab @ Biohub is hiring an Optical Engineer (Advanced Light Sheet Microscopy). 🧪🔬💻🔧 #Hardware + #Python + Advanced #Optics job-boards.greenhouse.io/biohub/jobs/...

Optical Engineer, Advanced Light Sheet Microscopy

San Francisco, CA (Hybrid)

job-boards.greenhouse.io

Join us this Friday, May 29 at 12:00 CET for a #MAIIA webinar! @haesleinhuepf.bsky.social shares his #bioImaging analysis insights zoom : u-paris.zoom.us/j/8906701496... ID: 89067014969 Pass: 285136 #AI #RTmfm @cnrs.fr

We look forward to expert contributions on the subtopic “Large Language Models and Knowledge Graphs” (LLMs & KGs) from @haesleinhuepf.bsky.social, @pascalhitzler.bsky.social, Yujia Hu, and Marco Valentino at the @scadsai.bsky.social Summer School this year. Read more: 👉 scads.ai/event/summer...

AI-agents write code for us, fix errors and try out other algorithms - tasks we data scientists do on a daily basis. But they can do it in parallel, all steps fully automatically. Check out %%alice & sand-bob #opensource! haesleinhuepf.github.io/sand-bob/exa...

%%alice 🥁

I was copying code and error messages between Jupyter and ChatGPT way too often, so I vibe-coded this little helper: github.com/haesleinhuep...

Thrilled to see @globias.bsky.social in Nature Methods! 🔬 Huge thanks to everyone who took the survey—more results are on the way!📊 Want to help? Join us to coordinate regional surveys or global efforts. Let’s build this community together!🤝 Read: www.nature.com/articles/s41... #GloBIAS #BioImage

GloBIAS@globias.bsky.social · 5mo ago

The GloBIAS Working Group survey 2024 has reached another important milestone with the publication of a short communication: GloBIAS: strengthening the foundations of bioimage analysis, in Nature Methods. doi.org/10.1038/s415... A big thank you to everyone involved Join GloBIAS at www.globias.org !

Small changes, massive speed gains. 🚀 The Array API standard is transforming Python performance, enabling 50x speedups by moving libraries like scikit-learn and SciPy to the GPU. Mateusz Sokół breaks down the latest benchmarks: buff.ly/ycoUlvD #GPUComputing #PythonProgramming #Innovation

I think it would be cool to link up all the Imaging/Analysis YouTube Channels in the "Featured Channels" section of HCBI's YouTube homepage. What are some of the best we could highlight?

LLMs are autoregressive and slow? No! Parallel Token Prediction decodes multiple consistent tokens in one model call. PTP allows arbitrary dependencies in one call, unlike discrete diffusion. Practical: 2.4x speedup github.com/mandt-lab/ptp ICLR: Apr 23, morning poster P3-#608

1/ 🔬🧑‍💻 Tired of going back and forth between GUIs and code for your 3D image analysis needs? Would you like to keep your focus in one place (notebook), without sacrificing interactivity? Here’s a tool that can help!

I teamed up with GitHub Copilot to make some fractal art… and I was not disappointed 😃 github.com/haesleinhuep...

Excited to launch the accompanying free RLHF Course for my book. To kick it off, I've released: - Welcome video - Lecture 1: Overview of RLHF & Post-training - Lecture 2: IFT, Reward Models, Rejection Sampling - Lecture 3: RL Math - Lecture 4: RL Implementation Landing page: rlhfbook.com/course

Course | RLHF Book by Nathan Lambert

Course lectures and talks on RLHF and post-training.

rlhfbook.com