Sign in

Ben Gallusser

@bengallusser.bsky.social
155 followers 452 following 20 posts

Deep Learning, Computer Vision, Biology

PostsRepliesMedia
Reposted by Ben Gallusser
Tamas Nagy @tamasnagy.com · 06/09/2026
Even with all the advancements in automated cell tracking getting us to 90%+ accuracy...that's still a lot of broken tracks over long movies! Our brains are pretty good at this so I made Vizsla 🐕, a little @napari.org plugin, to help you fix your tracks manually. 👉 pypi.org/project/napa...
13012
Reposted by Ben Gallusser
Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026
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
17941
Reposted by Ben Gallusser
Hacker News 300 @betterhn300.e-work.xyz · 19/05/2026
We let AIs run radio stations andonlabs.com/blog/andon-fm (news.ycombinator.com/item?id=481833…)
andonlabs.com
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.
001
Ben Gallusser @bengallusser.bsky.social · 17/03/2026
Love it, what a team 😍 For people solving the hardest problems in imaging data, look no further
031
Reposted by Ben Gallusser
Martin Weigert @maweigert.bsky.social · 02/03/2026
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
17030
Ben Gallusser @bengallusser.bsky.social · 12/02/2026
It's ok I guess I'll click on some cars or bikes to get my open-source PRs merged now
120
Ben Gallusser @bengallusser.bsky.social · 11/12/2025
🚀⭐️ 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...
2174
Reposted by Ben Gallusser
Jan Funke @janfunkey.bsky.social · 17/11/2025
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.org
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.,
1189
Ben Gallusser @bengallusser.bsky.social · 20/11/2025
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 🤖
imagej.net
TrackMate Trackastra
Trackastra integration in TrackMate.
1186
Reposted by Ben Gallusser
Misha Ahrens @mishaahrens.bsky.social · 08/09/2025
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...
319370
Reposted by Ben Gallusser
Egor Kotov 🌐🏃‍♂️🚊🚋🚙 @ekotov.pro · 23/08/2025
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...
medium.com
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…
195
Ben Gallusser @bengallusser.bsky.social · 30/07/2025
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.
15317
Ben Gallusser @bengallusser.bsky.social · 10/07/2025
Looking for a great PhD position? I had the pleasure of doing my doctoral research in Martin’s group - wholeheartedly recommended :)
030
Reposted by Ben Gallusser
Albert Dominguez Mantes @albertdm.bsky.social · 06/06/2025
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)
rdcu.be
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...
35524
Reposted by Ben Gallusser
Talley Lambert @talley.codes · 22/04/2025
github.com/hxu296/tariff
github.com
GitHub - hxu296/tariff: The official repository for tariff
The official repository for tariff. Contribute to hxu296/tariff development by creating an account on GitHub.
062
Ben Gallusser @bengallusser.bsky.social · 04/04/2025
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.
260