Albert Dominguez Mantes (@Albertdm99) header
Albert Dominguez Mantes (@Albertdm99) profile picture

Albert Dominguez Mantes

@Albertdm99

PhD student @EPFL developing computational methods for microscopy images || BSc in Data Science @la_UPC

 Lausanne, Switzerland
Joined September 2017
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Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)Photo by Albert Dominguez Mantes (@Albertdm99)
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @naturemethods! Since the pre-print, we have added many cool features, notably native 3D detection! @martweig @GioeleLaManno @epflSV @EPFL_Imaging Paper: rdcu.be/epIB7 (1/N)
Martin Weigert (maweigert.bsky.social) (@martweig) profile pictureMartin Weigert (maweigert.bsky.social)@martweig6 Feb 2024
Excited to share Spotiflow, our new spot detection method for image-based spatial transcriptomics that facilitates the analysis of large iST images. Lead by @Albertdm99 jointly w @GioeleLaManno @epflSV @EPFL_Imaging @EPFL_BioE biorxiv.org/content/10.1101/… github.com/weigertlab/spotif…
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EPFL Center for Imaging (@EPFL_Imaging) profile picture
EPFL Center for Imaging@EPFL_Imaging12 Jun 2025
🧬🔬 Millions of molecules automatically detected in human tissues thanks to Spotiflow, a revolutionary AI-powered microscopy tool developed at @EPFL and @tudresden_de 👇 📍Supported by @EPFL_Imaging 🔗actu.epfl.ch/news/in-the-bli… #AI #Microscopy #SpatialBiology #OpenScience #EPFL
Image from EPFL Center for Imaging (@EPFL_Imaging)
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Nature Methods (@naturemethods) profile picture
Nature Methods@naturemethods6 Jun 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. nature.com/articles/s41592-0…
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereograp...

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereograp...

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...

nature.com
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For more details on using Spotiflow, check our repository at github.com/weigertlab/spotif…! We are very excited to see what uses cases people will find for Spotiflow! (9/N)
GitHub - weigertlab/spotiflow: Accurate and efficient spot detection for microscopy data

GitHub - weigertlab/spotiflow: Accurate and efficient spot detection for microscopy data

Accurate and efficient spot detection for microscopy data - weigertlab/spotiflow

github.com
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A massive thanks to all the incredible people who contributed to this work, it's been an amazing ride! And a shoutout to all the people who have tried already tried Spotiflow and provided feedback, it's truly great to see the community using it :) (N/N)
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ScaDS.AI Dresden/Leipzig (@Sca_DS) profile picture
ScaDS.AI Dresden/Leipzig@Sca_DS6 Jun 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-detectio… Find the publication in Nature Methods: 👉 nature.com/articles/s41592-0…
Image from ScaDS.AI Dresden/Leipzig (@Sca_DS)
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Dr. Bernadette Stolz (@StolzBernadette) profile picture
Dr. Bernadette Stolz@StolzBernadette10 Oct 2024
🚨OPEN PhD position🚨 I am looking for a highly motivated PhD student to join my project group in the Department of Machine Learning and Systems Biology @MLSB_Borgwardt led by @kmborgwardt at @MPI_Biochem near Munich. Deadline November 15th. Please RT.
Max Planck Institute of Biochemistry (MPIB) (@MPI_Biochem) profile pictureMax Planck Institute of Biochemistry (MPIB)@MPI_Biochem10 Oct 2024
Are you enthusiastic about developing new methods in topological #DataAnalysis and #MachineLearning to solve problems in the #LifeSciences? Join @StolzBernadette and her project group! ❗️ Apply until November 15 ❗️ mpg.de/23545575/phd-student-…
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Gioele La Manno (@GioeleLaManno) profile picture
Gioele La Manno@GioeleLaManno22 Aug 2024
Interested in navigating #metabolism in space and time? Meet uMAIA (the Unified Mass Imaging Analyzer) - a framework developed in collaboration with @Gio_Dangel0 & @OatesLab @epflSV led by @HSchede & @Leila_Alieh #omics #lipidtime #MALDI biorxiv.org/content/10.1101/… 1/N
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Just accepted at ECCV 24 🎉🎉 big congrats to @bengallusser ! Milano in autumn it is then...
Martin Weigert (maweigert.bsky.social) (@martweig) profile pictureMartin Weigert (maweigert.bsky.social)@martweig31 May 2024
Happy to present Trackastra - a new transformer-based cell tracking method that aims to reduce manual parameter tuning in tracking experiments while yielding SOTA results on several datasets. Great work by @bengallusser @epflSV arxiv.org/abs/2405.15700 github.com/weigertlab/tracka…
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Ben Gallusser (@bengallusser) profile picture
Ben Gallusser@bengallusser19 Jun 2024
Happy to share our group's work together with @Albertdm99 on DL-based spot detection and cell tracking today at the great Swiss BioImage Analysts' Society meeting @SwissBIAS, so many cool projects around!
Image from Ben Gallusser (@bengallusser)
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James Manton (@JamesDManton) profile picture
James Manton@JamesDManton13 Jun 2024
We present: 'Multispectral live-cell imaging with uncompromised spatiotemporal resolution'. biorxiv.org/content/10.1101/… 1/16
Multispectral live-cell imaging with uncompromised spatiotemporal resolution

Multispectral live-cell imaging with uncompromised spatiotemporal resolution

Multispectral imaging is an established method to extend the number of colours usable in fluorescence imaging beyond the typical limit of three or four, but standard approaches are poorly suited to...

biorxiv.org
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Florian Jug (@florianjug) profile picture
Florian Jug@florianjug6 Jun 2024
Another year, another #BIC Workshop! This year at @eccvconf 2024 in Milan, 🇮🇹. Check it out here: bioimagecomputing.com Submission Deadline: July 19th  Get your computational work out, we are looking forward to meet you in October! 🍕 🍷 👩‍🎓 👨‍🎓 ☀️
Image from Florian Jug (@florianjug)
Image from Florian Jug (@florianjug)
Image from Florian Jug (@florianjug)
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Ben Gallusser (@bengallusser) profile picture
Ben Gallusser@bengallusser31 May 2024
Excited to share Trackastra, our new study on generalizable data-driven cell tracking. We use a lean transformer to learn costs for linking up segmented cells into lineages. - Preprint: arxiv.org/abs/2405.15700 - Napari plugin with first pretrained models: github.com/weigertlab/napari…
Martin Weigert (maweigert.bsky.social) (@martweig) profile pictureMartin Weigert (maweigert.bsky.social)@martweig31 May 2024
Happy to present Trackastra - a new transformer-based cell tracking method that aims to reduce manual parameter tuning in tracking experiments while yielding SOTA results on several datasets. Great work by @bengallusser @epflSV arxiv.org/abs/2405.15700 github.com/weigertlab/tracka…
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