Seeing our good old AURA-Net from 2021 (doi.org/10.1109/ISBI...) end up 2nd on a 2025 U-Net variants leaderboard was not on my bingo card for this year, but here we are (source: doi.org/10.48550/arX...)

JupyterCon!

This is the eXplainable AI research channel of the machine learning group of Prof. Klaus-Robert Müller at Technische Universität Berlin @tuberlin.bsky.social & BIFOLD @bifold.berlin. Let's connect! #XAI #ExplainableAI #MechInterp #MachineLearning #Interpretability

#GloBIAS2025 is ongoing with amazing speaker lineups at Kobe city Beautiful location, amazing food and warm bioimage analysis community. What wlse does one need? 😊 Thanks to @globias.bsky.social for this event

Using #LLMs for science👨‍💻💬? We have a fun tool for you: introducing #folder2md4llms. It converts an entire folder of docs/code/pdfs/pptx into a single markdown file that you can upload to your chatbot of choice. We use it to talk with our publications database or code repos github.com/HenriquesLab...

We just released "German Commons", the largest openly-licensed German text dataset for LLM training: 154B tokens with clear usage rights for research and commercial use. huggingface.co/datasets/coral-nlp/german-commons

Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !

I just finished my @unileipzig.bsky.social #LunchLecture. Thanks everyone for the vivid discussion and Nicole Koburger for hosting us! The slides are online #openaccess 🧑‍🏫🔓 zenodo.org/records/1742...

One more open position at the Data Science Centre here! This one is working on our recently open-sourced ELN/LIMS/all-in-one solution LabID (gitlab.com/lab-integrat...). If you have either full stack or scientific workflows experience, check it out! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Missed our #ScaDSAIMeetup on AI insights into the Model Context Protocol (#MCP)?  All talks, workshop materials & repos are now on #Zenodo! 🎤 Talks: https://doi.org/10.5281/zenodo.17158643 🛠️ Workshop: https://zenodo.org/records/17158770"

The next @unileipzig.bsky.social's  #LunchLectures will take place on October 23, this time featuring @haesleinhuepf.bsky.social  from @scadsai.bsky.social . He will give a lecture on “How generative AI influences research and teaching.” 👉 https://f.mtr.cool/srahlhpary

As part of our monthly meeting, we do a run-down of all* the new #bioimageanalysis tools that have been published in the last couple of weeks on BioRxiv**, so I thought I'd start sharing here as well. *I will miss some, apologies if I miss your paper

Together with the @iom-leipzig.bsky.social, @haesleinhuepf.bsky.social & Matthias Täschner hosted the #AISchool2025 last week in Leipzig. The Materials were provided by @scadsai.bsky.social#AISchool2025 👉 https://f.mtr.cool/yzmimoxbvz #MachineLearning #DataVisualization #HPCWorkflows

Data Management Plan: * We will keep all data and literature in open browser tabs sychronized between the computers of all project members using the same Google Chrome profile. * By the end of the project we publish the username and password of that profile under a CC-BY 4.0 license.

"LLMs are here to stay. [...] The best developers won’t be the ones who write every line by hand." 👍

🚀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

#Forschungsbewertung im Fokus Die Veranstaltung am 10.09.25 bot Raum für Austausch: Warum sind Reformen nötig? Welche Chancen und Herausforderungen ergeben sich daraus? Und welchen Mehrwert bietet eine Mitgliedschaft in der internationalen CoARA – Coalition for Advancing #ResearchAssessment?

The next @scadsai.bsky.social Meetup on October 21 will give you the chance to learn more about two highly topical fields of AI application: "Sovereign GenAI & Research Agents in Practice". Register here, join the meetup community and share your ideas:  👉 https://scads.ai/event/meetup/

🥇Congratulations to Filippo de Bortoli from @scadsai.bsky.social, who attended the #FroCoS2025 in Reykjavík, Iceland. He won the Best Student Paper Award for a paper co-authored with @scadsai.bsky.social PI Prof. Franz Baader. Read more about the paper: 👉 https://f.mtr.cool/yegcmotvkl

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...

Second, for a Mathematical Modeling Specialist - this person will consult and collaborate in projects, but also engage in training and establishing a community of practice. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

OpenAI proudly declared that Codex had written 80% of the UI for their Agent Builder. The UI...

I'm in the middle of a data science training and I just observed how a trainee copy-pasted one of our exercises to ChatGPT to solve it 😊

I gave a talk today at The Curve on the state of open models. Here are the slides, recording soon. Topics include: Chinese ecosystem, reflections on DeepSeek, the demise of Llama, who will fill the U.S. market, what local models do, ATOM project & ai2, and more topics buff.ly/8BiC67C

Here it is! Postdoctoral position to identify the progenitors sensory organs in the regenerating legs of Parhyale apply here: www.averof-lab.org/pages/tracman 1/3

For academic purposes, I generated 100 UMAPs from the same tabular raw data, I sorted them and the result looks too funny to not share it with you 😃 haesleinhuepf.github.io/BioImageAnal...

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social! Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬 📅 Applications open Oct 6 (deadline: ~Oct 27) 📍 San Sebastian, Spain. 👉 cvpd.github.io/post/2025-09...

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-...

Nice to see another fully open, multimodal LM released! Good license, training code, pretraining data, all here. LLaVA-OneVision-1.5: Fully Open Framework for Democratized Multimodal Training Slowly, the community is growing. arxiv.org/abs/2509.236...

@scadsai.bsky.social training coordinator @haesleinhuepf.bsky.social provided insights into his professional career in the podcast series “The Microscopists.” If you want to know why he'll never ask biologists for better images again, click here: 🍍 themicroscopists.bitesizebio.com/episodes/rob...

How do I manage my #ResearchSoftware? 🤔  Get the #OpenAccess presentation by Matthias Täschner and @haesleinhuepf.bsky.social#ResearchSoftware?#OpenAccesswhich was created as part of the #DevOps hands-on training at #DataWeek2025.  👉 Find out about version control, collaborative working and much more: 10.5281/zenodo.15654888

Wir hatten heute am Institut ein hervorragendes KI-Training für die Psychologie mit vielen praktischen Tipps, durchgeführt von @haesleinhuepf.bsky.social 👌🏼 Die Materialien sind online verfügbar, falls jemand reinschauen möchte: scads.github.io/ai4psycholog...

Nature Biomedical Engineering is hiring again! This time we're hoping to add an editor with machine learning expertise to the team (although we are open to those with other relevant expertise!) Deadline is Oct 20. Please RT! springernature.wd3.myworkdayjobs.com/SpringerNatu...

Link to HHMI preprint mandate hhmicdn.blob.core.windows.net/policies/Imm...

Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇

Are you easily able to provide details on any #data point and processing steps if you get a mean question by reviewer 2? Do you plan to publish #FAIR data? Let's talk about #DataManagement tips & tricks in active projects! @unibergen.bsky.social library webinar Sept 26th: www.uib.no/en/ub/178969...

Oh yes-the one and only Robert Haase @haesleinhuepf.bsky.social From #GrandTheftAuto to the impact AI is having on #bioimaging. +the challenges of creating AI courses for bioimage analysis, & his unique perspective as a programmer-turned-biologist. Stream- bit.ly/microscopist... @globias.bsky.social

I gave two seminars at @embl.org Heidelberg these days: One about using LLMs via #biabob for #BioImageAnalysis and one about how LLMs impact BioImage #DataScience Thanks EMBL for having me! Materials #openaccess 🧑‍🏫🖥️🔓 zenodo.org/records/1705... zenodo.org/records/1710... scads.github.io/llm-bia-2025

Paper alert!🧪 We derive a theory that underpins interface resistance with a physical foundation and look at how it changes droplet growth and recovery kinetics! Awesome collab with @bosste.bsky.social Tyler Harmon @hymanlab.bsky.social @m-pol.bsky.social and Frank Jülicher @mpipks.bsky.social 1/4

If you want to get started, here's a tutorial that I made: github.com/JoachimGoedh... Reach out if you have questions or want advice!!

(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...

Do NOT perform "image enhancement" with LLMs or AI for any forensic purposes whatsoever. The people doing this have no clue of how images are formed, nor of how AI/LLM image manipulations function. AI/LLMs introduce *NEW DATA* that leads to mis/dis information.

I'm sitting in a train with internet connection quality like everyone would expect it in central Germany, and I would like to thank ollama.com for its existence! 🤩 This response (< 5min, video in real-time) is generated using #ollama running locally on my laptop with 32GB Ram and an RTX 4070 GPU 🤯

Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth. embl.wd103.myworkdayjobs.com/en-US/EMBL/j... (1/3)

🫠

The materials from the “Reproducible Bio-Image Analysis using #Python, #Napari, #Jupyter, and #AI” workshop, run by @haesleinhuepf.bsky.social as part of the @embo.org Course on #LightSheetMicroscopy, are now available #OpenAccess! 📗 scads.github.io/embo-lsm-bia... 📕 zenodo.org/records/1681...

Common mistake in LLM prompting projects: jumping into full-scale pipelines (datasets and inference) without testing feasibility. Iterating at scale is expensive and time-consuming. Start with ONE example to validate the hypothesis, verify context, debug the design, then scale.