Ben Gallusser
@bengallusser.bsky.social
Deep Learning, Computer Vision, Biology
Reposted by Ben Gallusser
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/...
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/...
November 17, 2025 at 7:44 PM
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/...
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/...
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 🤖
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 🤖
November 20, 2025 at 8:18 PM
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 🤖
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 🤖
Reposted by Ben Gallusser
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...
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...
September 8, 2025 at 4:25 PM
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...
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...
Reposted by Ben Gallusser
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
August 23, 2025 at 10:09 AM
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...
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.
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.
July 30, 2025 at 8:15 AM
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.
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 :)
I had the pleasure of doing my doctoral research in Martin’s group - wholeheartedly recommended :)
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
Vacancy ID 12244
www.verw.tu-dresden.de
July 10, 2025 at 6:54 PM
Looking for a great PhD position?
I had the pleasure of doing my doctoral research in Martin’s group - wholeheartedly recommended :)
I had the pleasure of doing my doctoral research in Martin’s group - wholeheartedly recommended :)
Reposted by Ben Gallusser
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)
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
June 6, 2025 at 6:58 PM
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)
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)
Reposted by Ben Gallusser
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.
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.
April 4, 2025 at 12:49 AM
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.
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.