Albert Dominguez Mantes
@albertdm.bsky.social
π€ 122
π₯ 114
π 15
PhD student @ EPFL in computer vision for microscopy | Prev Data Science @ UPC
pinned post!
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
! π₯οΈ:
github.com/weigertlab/muvit
π:
arxiv.org/abs/2602.24222
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3 months ago
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Albert Dominguez Mantes
Image Cooperative
2 months ago
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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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
! π₯οΈ:
github.com/weigertlab/muvit
π:
arxiv.org/abs/2602.24222
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3 months ago
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Albert Dominguez Mantes
Martin Weigert
3 months ago
Excited to share our new paper (CVPR 2026 π): "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
3 months ago
π£Weβre back π¬ππ₯οΈ!
#CBIAS2026
returns 23β24 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
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Crick BioImage Analysis Symposium 2026
https://www.crick.ac.uk/whats-on/crick-bioimage-analysis-symposium-2026
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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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4 months ago
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Albert Dominguez Mantes
Crick BioImage Analysis Symposium
6 months ago
Now speaking
#CBIAS2025
@albertdm.bsky.social
from
@maweigert.bsky.social
introducing spotiflow
www.nature.com/articles/s41...
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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!
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6 months ago
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Albert Dominguez Mantes
Anna Foix
7 months ago
Weβve upgraded ShapeEmbed π 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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Albert Dominguez Mantes
Gioele La Manno
7 months ago
π§ 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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Albert Dominguez Mantes
Virginie Uhlmann
8 months ago
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 πΎ Catch her at
@neuripsconf.bsky.social
to find out more!!
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Albert Dominguez Mantes
Anna Foix
8 months ago
Happy to share that ShapeEmbed has been accepted at
@neuripsconf.bsky.social
π 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 π
arxiv.org/pdf/2507.01009
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Albert Dominguez Mantes
Ryan Savill
9 months ago
(1/14) Iβm happy and proud to introduce: SpinePy β 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 DβAngelo
9 months ago
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
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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.
https://www.nature.com/articles/s41592-025-02771-7.epdf?sharing_token=K5iHw1c3Jkq0HBI6pQtJNdRgN0jAjWel9jnR3ZoTv0O0dqgsACWV1axX8CzMM4T7iI1XKGp3N-81HgCRS-XXxftpPp3pUNuwYw1DBxUrNsq_lsZHO-zWSflih1WxTQah_5HFsLyD8DN9QPvkFm6CzdtR5nIyDK9dJegr1uk_77g%3D
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Albert Dominguez Mantes
Nicolas Chiaruttini
10 months ago
A new extension! RΓ©my made a wrapper of
@albertdm.bsky.social
+
@maweigert.bsky.social
's Spotiflow (2/3)
forum.image.sc/t/qupath-ext...
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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 π ! This extension reproduces the logic behind the qupath-extension-cellpose to ...
https://forum.image.sc/t/qupath-extension-spotiflow-is-now-available/115646
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Albert Dominguez Mantes
Ben Gallusser
10 months ago
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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Working in Martinβs group is an amazing experience, donβt hesitate to apply and reach out if you have any questions!
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11 months ago
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Albert Dominguez Mantes
Martin Weigert
12 months ago
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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Albert Dominguez Mantes
Nature Methods
12 months ago
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...
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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...
https://www.nature.com/articles/s41592-025-02662-x?utm_source=twitter&utm_medium=social&utm_campaign=nmeth
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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)
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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...
https://rdcu.be/epIB7
12 months ago
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Albert Dominguez Mantes
ScaDS.AI Dresden/Leipzig
12 months ago
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: π
scads.ai/transcript-d...
Find the publication in Nature Methods: π
www.nature.com/articles/s41...
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AI Method Improves Transcript Detection in Microscopy Images
Spotiflow improves large-scale transcript localization by combining deep learning with a novel geometric detection approach.
https://scads.ai/transcript-detection-in-microscopy-images/
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Albert Dominguez Mantes
Jan Funke
about 1 year ago
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 π¨ April 30 π¨ Read on for more! π
www.mbl.edu/education/ad...
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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...
https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/aimbl-machine-learning-microscopy-image-analysis
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Albert Dominguez Mantes
Florian Jug
over 1 year ago
π¬π€ As pre-announced a few days ago... please let us proudly present to you: π΄πππππππππ - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. π¬
doi.org/10.1101/2025...
Like β€οΈ, repost π, and most importantly... please send feedback βοΈ our way! π
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