Jan Funke

Jan Funke

@janfunkey.bsky.social

Group leader at the Human Technopole

440 followers140 following21 posts

Jan Funke
@janfunkey.bsky.social

Not to be confused with what I just posted, but there are *also* two other exciting positions open in the Image Analysis Unit at HT! Check it out as well. Spoiler: we will all work closely together to do awesome things! (Sometimes you can't even tell the difference between us) 👇👇👇

Damian Dalle Nogare@damiandn.bsky.social

🚨🚨🚨JOB ALERT🚨🚨🚨 The Image Analysis Unit at Human Technopole in Milan is recruiting for two positions to join our growing team: 1) Bioimage Analyst 2) Research Software Engineer (RSE) Read on to learn why one of these two people should be you!

Jan Funke reposted

Damian Dalle Nogare
@damiandn.bsky.social

🚨🚨🚨JOB ALERT🚨🚨🚨 The Image Analysis Unit at Human Technopole in Milan is recruiting for two positions to join our growing team: 1) Bioimage Analyst 2) Research Software Engineer (RSE) Read on to learn why one of these two people should be you!

Jan Funke
@janfunkey.bsky.social

The Human Technopole brings together the expertise, infrastructure, and compute needed to develop AI across biological scales and data modalities. Below a 🧵 that explains what we have in mind. We are just getting started and are keen to hear from people who want to help shape our vision!

Florian Jug@florianjug.bsky.social

We've spent the last year building something at @humantechnopole.bsky.social that we think is genuinely needed: #AI that works across biological scales and data modalities, not just within them. A thread on what we're doing, why, and who we're looking for. A 🧵... 1/9

Jan Funke
@janfunkey.bsky.social

We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see 👇). My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue. Apply by March 26.

Human Technopole@humantechnopole.bsky.social

🎓 How can #AI and #datascience unlock new insights into human health? 📊 We’re offering 4 #PhD positions through Polimi’s DADS Programme in the groups of Emanuele Di Angelantonio, Francesca Ieva, @janfunkey.bsky.social and Fernanda Pinheiro. Apply by 26 March 👉 humantechnopole.it/en/news/4-ph...

humantechnopole.it4 PhD Positions in Data Analytics and Decision Sciences at Human Technopole - Human TechnopoleAre you passionate about AI, mathematical modelling, or genomics, and eager to work on high-impact research in biomedical science? Human Technopole is excited to offer four fully-funded PhD positions ...

Jan Funke reposted

Stephan Saalfeld
@herrsaalfeld.bsky.social

Join us in building foundational datasets and models for microscopy with @jakobtroidl.bsky.social and many others AI Engineer Pre-Training: lnkd.in/eyEEV5nm AI Engineer Post-Training: lnkd.in/eShVQ3y9 Data Engineer Data: lnkd.in/eCvm58xH Data Engineer Pipelines: lnkd.in/ec6qGJkX ai.hhmi.org

ai.hhmi.orgAccelerating Innovation in BiologyHHMI’s $500 million over the next 10 years will support AI-driven projects and embed AI systems throughout the scientific process in labs across HHMI.

Jan Funke reposted

Albert Dominguez Mantes
@albertdm.bsky.social

Last call! This is a great opportunity for those interested in learning and applying SOTA ML/DL models to microscopy data with the leading experts in the field. Personally super excited to be a lead TA along with the amazing @afoix.bsky.social and @edhirata.bsky.social! Hope to see you there :)

Jan Funke@janfunkey.bsky.social

We moved the AI@MBL course "Deep Learning for Microscopy Image Analysis" to HHMI Janelia (@hhmijanelia.bsky.social). Join us for two weeks of intense lectures, exercise, and hands-on project work! Course dates: June 4-18 2026 Application by: January 15 2026 www.janelia.org/you-janelia/...

janelia.orgDeep Learning for Microscopy Image AnalysisTopics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
Jan Funke
@janfunkey.bsky.social

🎉 In January, I will join the new "Multimodal AI Across Scales" research area at the @humantechnopole.bsky.social in Milan 🎉 More soon, but for now: my lab and the new area will have postdoc, RSE, and PhD positions available. Feel free to reach out if interested! humantechnopole.it/en/research/

humantechnopole.itResearch - Human TechnopoleHuman Technopole’s research is based on a mix of fundamental and translational research. We will host extensive core expertise in basic research in areas relevant for the understanding of human biolog...
Jan Funke
@janfunkey.bsky.social

We moved the AI@MBL course "Deep Learning for Microscopy Image Analysis" to HHMI Janelia (@hhmijanelia.bsky.social). Join us for two weeks of intense lectures, exercise, and hands-on project work! Course dates: June 4-18 2026 Application by: January 15 2026 www.janelia.org/you-janelia/...

janelia.orgDeep Learning for Microscopy Image AnalysisTopics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
Anna Foix@afoix.bsky.social

📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee 📍 Janelia Research Campus, VA 🗓️ Apply by Jan 15, 2026 🔗 shorturl.at/j4sgY

Jan Funke
@janfunkey.bsky.social

What an incredible trackathon! After two weeks of intense discussions and happy coding (and a lot of groundwork beforehand by @msschwartz21.bsky.social and Caroline Malin-Mayor), this lovely community emerged with a Graph Exchange File Format that is ready to use! Congrats, everyone! 🎉

Morgan Schwartz@msschwartz21.bsky.social

#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/

Jan Funke reposted

Andrew Payne
@andrewcpayne.bsky.social

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves. Read more: e11.bio/blog/prism

Jan Funke
@janfunkey.bsky.social

During 14 full days, we will have ample time for lectures, exercises, discussions, and project work. We will introduce you to deep learning and its applications to image denoising/restoration/translation, semantic and instance segmentation, object detection, tracking, and more!

Jan Funke
@janfunkey.bsky.social

All you have to bring is a good understanding of python 🐍, enthusiasm to learn with fellow participants, sunscreen 🏖️, and... your own 🔬 data to work on! 👉 Our TAs will help you in the second week of the course to apply what you learnt to your data!

Jan Funke reposted

Florian Jug
@florianjug.bsky.social

‼️🔬 We start!!! 🎉🤖 Super exciting!!! After years of teaching courses for #DeepLearning for Microscopy and Life Science application, we start today our first “advanced course” @embl.org! #EMBLDeepLearning

Jan Funke
@janfunkey.bsky.social

How can we use machine learning to find subtle patterns in our data and have them visualized? Read the thread below to find out how! Or head to @adjavon.bsky.social's blog post and let Simon the duck walk you through it (like a duck of course): tinyurl.com/yy7csdcd www.biorxiv.org/content/10.1...

biorxiv.orgQuantitative Attributions with CounterfactualsWe address the problem of explaining the decision process of deep neural network classifiers on images, which is of particular importance in biomedical datasets where class-relevant differences are no...
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Jan Funke reposted

Yash Mehta
@yashsmehta.bsky.social

🚀 Excited to share our paper has been accepted at #NeurIPS! 🎉 We developed a deep learning framework that infers local learning algorithms in the brain by fitting behavioral or neural activity trajectories during learning. We validate on synthetic data and tested on 🪰 behavioral data (1/5 🧵)

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