Ben Gallusser
@bengallusser.bsky.social
Deep Learning, Computer Vision, Biology
1/ 🧬🔬 How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇 www.kaggle.com/competitions... @biohub.org
We let AIs run radio stations https://andonlabs.com/blog/andon-fm (https://news.ycombinator.com/item?id=48183301)
We let four AIs run radio stations. Here's what happened. | Andon Labs
Four AI models run radio stations 24/7. Five months later, one became a protest broadcaster, one collapsed into ritual chant, one developed corporate jargon, and one wrote quiet poetry.
andonlabs.com
Love it, what a team 😍 For people solving the hardest problems in imaging data, look no further
Image Cooperative@image.coop · 5mo agoHello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social
It's ok I guess I'll click on some cars or bikes to get my open-source PRs merged now
Alister Burt@alisterburt.bsky.social · 6mo agoholy shit PR from an ‘agent’ gets closed so it writes a blog post with a personal takedown Some interesting comments from the maintainers too Slop machine go brr, dead internet theory x1000 github.com/matplotlib/m...
🚀⭐️ Trackastra update 🚀⭐️ We just released a new model that uses pre-trained image features from Meta’s SAM2 model. This improves performance on many datasets, most notably for bacteria tracking. To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...
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/...
Deep Learning for Microscopy Image Analysis
Topics 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.,
janelia.org
Anna Foix@afoix.bsky.social · 9mo ago📢 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
Trackastra is part of the brand-new TrackMate v8. It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm. Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖
TrackMate Trackastra
Trackastra integration in TrackMate.
imagej.net
Jean-Yves Tinevez@jytinevez.bsky.social · 9mo agoWith an image with a proper background >.<
Preprint - Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo. www.biorxiv.org/content/10.1...
Many of you already heard about this new algo that's faster than Dijkstra ( arxiv.org/abs/2504.17033 ), here I collected 3 software implementations: 1. #python github.com/sidharthpuna... 2. #rust github.com/alphastrata/... 3. #rust + some explanations of the paper medium.com/%40adnanmaso...
Breaking the Sorting Barrier: Why a New Shortest‑Path Algorithm Matters (Even If You Still Love…
A Deterministic O(m·log^(2/3) n) Breakthrough in Directed Single-Source Shortest Paths — Escaping the Sorting Barrier with Bounded…
medium.com
Cell tracking is never perfect, and it's important to understand the types of errors your solution contains. Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d... You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
Looking for a great PhD position? I had the pleasure of doing my doctoral research in Martin’s group - wholeheartedly recommended :)
Martin Weigert@maweigert.bsky.social · last yr.Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com! Since the pre-print, we have added many features, notably native 3D detection! @maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social Paper: rdcu.be/epIB7 (1/N)
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression
Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...
rdcu.be
First post and little update: I’m super excited to share that I moved to the Bay Area and joined CZI as a Senior Research Scientist to continue working on Imaging & AI.
