Albert Dominguez Mantes
@albertdm.bsky.social
π€ 98
π₯ 120
π 11
PhD student @ EPFL in computer vision for microscopy | Prev Data Science @ UPC
pinned post!
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
5 months ago
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Albert Dominguez Mantes
Anna Foix
22 days 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
23 days 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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Virginie Uhlmann
about 2 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!!
add a skeleton here at some point
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Anna Foix
about 2 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
(1/N)
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Ryan Savill
about 2 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
2 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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Nicolas Chiaruttini
3 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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Ben Gallusser
3 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!
add a skeleton here at some point
4 months ago
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Martin Weigert
5 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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Nature Methods
5 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)
loading . . .
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
5 months ago
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reposted by
Albert Dominguez Mantes
ScaDS.AI Dresden/Leipzig
5 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
7 months 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
9 months 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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