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Albert Dominguez Mantes

@albertdm.bsky.social
131 followers 116 following 15 posts

PhD student @ EPFL in computer vision for microscopy | Prev Data Science @ UPC

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Reposted by Albert Dominguez Mantes
Anna Foix @afoix.bsky.social · 09/07/2026
🚨🚨🚨 DEADLINE EXTENSION ALERT! 🚨🚨🚨 Great news 🧬💻 The submission deadline for the BioImage Computing (BIC) Workshop at @eccv.bsky.social is now July 20, 2026! We can't wait to see your latest research! 🔬👩‍💻👨‍💻 🚪 Submit: openreview.net/group?id=the... 🌐 Info: www.bioimagecomputing.com
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Anna Foix @afoix.bsky.social · 15/06/2026
BIC @eccv.bsky.social 2026 is OPEN! Show us your new CV, AI & Bio work🦠🔬 🚪: openreview.net/group?id=the... Thanks organisers for making it possible @alex-krull.bsky.social Peter Bajcsy @janfunkey.bsky.social @florianjug.bsky.social Qingjie Meng @virginieuhlmann.bsky.social @maweigert.bsky.social ✨
openreview.net
ECCV 2026 Workshop BIC
Welcome to the OpenReview homepage for ECCV 2026 Workshop BIC
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Anna Foix @afoix.bsky.social · 14/06/2026
We work hard but also we have a lot of fun together @albertdm.bsky.social @edhirata.bsky.social #dljanelia2026
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Anna Foix @afoix.bsky.social · 14/06/2026
So lucky to have such brilliant friends doing an absolutely smashing job! Do check out MuViT by @albertdm.bsky.social and @maweigert.bsky.social , released at #CVPR2026 for multi-scale resolution images 🔬✨ #DLforBiology #DLJanelia2026 🐙: github.com/weigertlab/m... 📄: arxiv.org/abs/2602.24222
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Jan Funke @janfunkey.bsky.social · 05/06/2026
And so it begins! Day 1, Lecture 0 of the first DL for Microscopy Image Analysis course at @hhmijanelia.bsky.social. Slides from @florianjug.bsky.social, presented by our TA Federico Carrara. #dljanelia
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Image Cooperative @image.coop · 16/03/2026
Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
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Albert Dominguez Mantes @albertdm.bsky.social · 02/03/2026
Very happy that MuViT, our (CVPR 2026!) work on learning across spatial scales in microscopy w transformers, is out! Check Martin's thread for a nice walkthrough :) Big thanks to my advisors @maweigert.bsky.social @gioelelamanno.bsky.social! 🖥️: github.com/weigertlab/muvit 📜: arxiv.org/abs/2602.24222
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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
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Crick BioImage Analysis Symposium @cbias.bsky.social · 25/02/2026
📣We’re back 🔬👀🖥️! #CBIAS2026 returns 23–24 November 2026: Join the bioimage analysis community to discuss advances in quantitative imaging & computational methods for image analysis. Great opportunity for early-career analysts & microscopists to present and connect. #CBIAS2026 #BioimageAnalysis
crick.ac.uk
Crick BioImage Analysis Symposium 2026
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Albert Dominguez Mantes @albertdm.bsky.social · 15/01/2026
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 :)
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Crick BioImage Analysis Symposium @cbias.bsky.social · 24/11/2025
Now speaking #CBIAS2025 @albertdm.bsky.social from @maweigert.bsky.social introducing spotiflow www.nature.com/articles/s41...
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Albert Dominguez Mantes @albertdm.bsky.social · 25/11/2025
Had a blast at #CBIAS2025! Great science (like the incredible ShapeEmbed talk from @afoix.bsky.social), amazing people and obviously tons of beautiful images :) Already looking forward to coming back next year!
Anna Foix giving a talk about ShapeEmbed at CBIAS2025
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Anna Foix @afoix.bsky.social · 17/10/2025
We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...
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Gioele La Manno @gioelelamanno.bsky.social · 16/10/2025
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution. www.biorxiv.org/cgi/content/...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 23/09/2025
You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!
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Anna Foix @afoix.bsky.social · 23/09/2025
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)
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Ryan Savill @cryaaa.bsky.social · 12/09/2025
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
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Giovanni D’Angelo @giodang.bsky.social · 03/09/2025
Happy to share our work on uMAIA, a framework for building metabolomic atlases from mass spectrometry imaging. With uMAIA, we mapped the lipidome of zebrafish development, uncovering spatially organized metabolic programs . www.nature.com/articles/s41... #developmentalbiology #MSI #lipidtime
nature.com
Unified mass imaging maps the lipidome of vertebrate development
Nature Methods - uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.
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Nicolas Chiaruttini @nkiaru.bsky.social · 12/08/2025
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3) forum.image.sc/t/qupath-ext...
forum.image.sc
QuPath extension Spotiflow is now available
Hello @qupath team & users, We are pleased to announce a new qupath-spotiflow-extension to handle spotiflow in QuPath 🎉 ! This extension reproduces the logic behind the qupath-extension-cellpose to ...
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Reposted by Albert Dominguez Mantes
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.
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Albert Dominguez Mantes @albertdm.bsky.social · 10/07/2025
Working in Martin’s group is an amazing experience, don’t hesitate to apply and reach out if you have any questions!
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Martin Weigert @maweigert.bsky.social · 06/06/2025
Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social www.nature.com/articles/s41... rdcu.be/epIB7
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Nature Methods @natmethods.nature.com · 06/06/2025
A nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...
nature.com
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 both iST and live imag...
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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...
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ScaDS.AI Dresden/Leipzig @scadsai.bsky.social · 06/06/2025
Get to know Spotiflow, an AI method that improves large-scale transcript localization by combining deep learning with a novel geometric detection approach. Learn more: 👉 scads.ai/transcript-d... Find the publication in Nature Methods: 👉 www.nature.com/articles/s41...
scads.ai
AI Method Improves Transcript Detection in Microscopy Images
Spotiflow improves large-scale transcript localization by combining deep learning with a novel geometric detection approach.
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Jan Funke @janfunkey.bsky.social · 18/04/2025
How can AI help you to analyze your microscopy images? Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6! Applications are due 🚨 April 30 🚨 Read on for more! 👇 www.mbl.edu/education/ad...
mbl.edu
AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory
The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks th...
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Florian Jug @florianjug.bsky.social · 11/02/2025
🔬🎤 As pre-announced a few days ago... please let us proudly present to you: 𝑴𝒊𝒄𝒓𝒐𝕊𝒑𝒍𝒊𝒕 - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. 🔬 doi.org/10.1101/2025... Like ❤️, repost 🔂, and most importantly... please send feedback ✉️ our way! 🙏
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