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Reposted by Ben Gallusser

Misha Ahrens @mishaahrens.bsky.social · Sep 8

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...

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Reposted by Ben Gallusser

Egor Kotov 🌐🏃‍♂️🚊🚋🚙 @ekotov.pro · Aug 23

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

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Ben Gallusser @bengallusser.bsky.social · Aug 18

So cool! Causal up until the penultimate layer, I bet the DiGradCam will look interesting. Also, as commonly known, if you can 3d print your neural network architecture you get to name it! GiuseppeNet ;) ?

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Ben Gallusser @bengallusser.bsky.social · Jul 31

I love that! A simple thing might be to spin out orthogonal to the major axis (of movement) in the few previous frames, and the sample could be rotated according to that. Not sure if our brains are ready to deal with that

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Ben Gallusser @bengallusser.bsky.social · Jul 30

Thanks @janfunkey.bsky.social and team for organizing this fun Hackathon for making open source software for science. Many of the other lit 🔥 cell tracking things we worked on are available at github.com/live-image-t....

Supplementary Video 6: TRACKASTRA results on bacteria compared to baselines

This is "Supplementary Video 6: TRACKASTRA results on bacteria compared to baselines" by Benjamin Gallusser on Vimeo, the home for high quality videos…

vimeo.com

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Ben Gallusser @bengallusser.bsky.social · Jul 30

Bonus: I added a 3D version, here is an example on the C. elegans dataset from the Cell Tracking Challenge.

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Ben Gallusser @bengallusser.bsky.social · Jul 30

With this visualisation one can intuitively compare different trackers

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Ben Gallusser @bengallusser.bsky.social · Jul 30

I originally made these when developing my tracking algorithm Trackastra www.ecva.net/papers/eccv_..., and have finally made them easy-to-produce for anyone at this year's @hhmijanelia.bsky.social Trackathon.

www.ecva.net

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Ben Gallusser @bengallusser.bsky.social · Jul 30

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.

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Ben Gallusser @bengallusser.bsky.social · Jul 10

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 · Jul 10

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

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Reposted by Ben Gallusser

Albert Dominguez Mantes @albertdm.bsky.social · Jun 6

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

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Reposted by Ben Gallusser

Talley Lambert @talley.codes · Apr 22

github.com/hxu296/tariff

GitHub - hxu296/tariff: The official repository for tariff

The official repository for tariff. Contribute to hxu296/tariff development by creating an account on GitHub.

github.com

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Ben Gallusser @bengallusser.bsky.social · Apr 4

Bonus: Recently, I also successfully finished my PhD at EPFL 🥳
It was as an incredible journey, thanks once more to everyone that helped making it a success :)

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Ben Gallusser @bengallusser.bsky.social · Apr 4

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.

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