Martin Weigert
@maweigert.bsky.social
Machine Learning for Microscopy | Prof @ TU Dresden | https://scholar.google.com/citations?user=ZltxyqoAAAAJ
Pinned
Martin Weigert
@maweigert.bsky.social
· Jun 6
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
www.nature.com/articles/s41...
rdcu.be/epIB7
Reposted by Martin Weigert
🧠 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/...
www.biorxiv.org/cgi/content/...
October 16, 2025 at 6:23 AM
🧠 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/...
www.biorxiv.org/cgi/content/...
Reposted by Martin Weigert
Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues.
The paper: arxiv.org/abs/2503.19545 1/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
October 9, 2025 at 12:56 PM
Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues.
The paper: arxiv.org/abs/2503.19545 1/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
Reposted by Martin Weigert
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:32 AM
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
Reposted by Martin Weigert
🧵1/14 Preprint thread! Can we predict a cell’s fate based on its dynamics? 🔮 Our new study unveils a framework for watching development unfold in real-time, revealing how a cell's shape and movement encode info about its future fate. 🔬📄 Preprint: tinyurl.com/4shf8v4x
September 22, 2025 at 9:37 AM
🧵1/14 Preprint thread! Can we predict a cell’s fate based on its dynamics? 🔮 Our new study unveils a framework for watching development unfold in real-time, revealing how a cell's shape and movement encode info about its future fate. 🔬📄 Preprint: tinyurl.com/4shf8v4x
Reposted by Martin Weigert
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
September 19, 2025 at 7:35 AM
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Reposted by Martin Weigert
(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...
September 12, 2025 at 12:44 PM
(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...
Reposted by Martin Weigert
Thanks Misha for the shout-out!
It has been a truly mind-opening journey. WHOLISTIC is one step towards whole-organism neuroscience and a true physiological observatory - with extensions on the way! I am continually amazed by what the data reveals - so much remains to be discovered and mined.
It has been a truly mind-opening journey. WHOLISTIC is one step towards whole-organism neuroscience and a true physiological observatory - with extensions on the way! I am continually amazed by what the data reveals - so much remains to be discovered and mined.
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...
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...
September 8, 2025 at 4:30 PM
Thanks Misha for the shout-out!
It has been a truly mind-opening journey. WHOLISTIC is one step towards whole-organism neuroscience and a true physiological observatory - with extensions on the way! I am continually amazed by what the data reveals - so much remains to be discovered and mined.
It has been a truly mind-opening journey. WHOLISTIC is one step towards whole-organism neuroscience and a true physiological observatory - with extensions on the way! I am continually amazed by what the data reveals - so much remains to be discovered and mined.
Reposted by Martin Weigert
Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy.
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)
September 5, 2025 at 3:37 PM
Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy.
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)
Reposted by Martin Weigert
How is this possible?
This ant can lay eggs of two different species, birthed by the same mother
This ant can lay eggs of two different species, birthed by the same mother
September 3, 2025 at 3:13 PM
How is this possible?
This ant can lay eggs of two different species, birthed by the same mother
This ant can lay eggs of two different species, birthed by the same mother
Reposted by Martin Weigert
Thrilled to share 🎉 I’m starting my lab at University of Zurich,
DMLS as Assistant Professor (tenure track) from Jan 2026!
The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬
DMLS as Assistant Professor (tenure track) from Jan 2026!
The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬
September 3, 2025 at 10:43 PM
Thrilled to share 🎉 I’m starting my lab at University of Zurich,
DMLS as Assistant Professor (tenure track) from Jan 2026!
The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬
DMLS as Assistant Professor (tenure track) from Jan 2026!
The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬
Reposted by Martin Weigert
Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...
Mechanical forces drive evolutionary change
A small tissue fold present in fruit fly embryos buffers mechanical stresses and may have evolved in response to mechanical forces.
www.mpi-cbg.de
September 3, 2025 at 3:26 PM
Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...
Reposted by Martin Weigert
EPFL, ETH Zurich & CSCS just released Apertus, Switzerland’s first fully open-source large language model.
Trained on 15T tokens in 1,000+ languages, it’s built for transparency, responsibility & the public good.
Read more: actu.epfl.ch/news/apertus...
Trained on 15T tokens in 1,000+ languages, it’s built for transparency, responsibility & the public good.
Read more: actu.epfl.ch/news/apertus...
September 2, 2025 at 11:48 AM
EPFL, ETH Zurich & CSCS just released Apertus, Switzerland’s first fully open-source large language model.
Trained on 15T tokens in 1,000+ languages, it’s built for transparency, responsibility & the public good.
Read more: actu.epfl.ch/news/apertus...
Trained on 15T tokens in 1,000+ languages, it’s built for transparency, responsibility & the public good.
Read more: actu.epfl.ch/news/apertus...
Reposted by Martin Weigert
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
With uMAIA, we mapped the lipidome of zebrafish development, uncovering spatially organized metabolic programs .
www.nature.com/articles/s41...
#developmentalbiology #MSI #lipidtime
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.
www.nature.com
September 3, 2025 at 10:40 AM
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
With uMAIA, we mapped the lipidome of zebrafish development, uncovering spatially organized metabolic programs .
www.nature.com/articles/s41...
#developmentalbiology #MSI #lipidtime
Reposted by Martin Weigert
Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 21, 2025 at 5:19 AM
Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Martin Weigert
📢We're #hiring Group Leaders!
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
August 26, 2025 at 7:00 PM
📢We're #hiring Group Leaders!
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
Reposted by Martin Weigert
Better ML for cryo-ET starts with better benchmarks.
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
doi.org
August 26, 2025 at 2:22 PM
Better ML for cryo-ET starts with better benchmarks.
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
Reposted by Martin Weigert
🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 25, 2025 at 9:06 AM
🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Martin Weigert
The Friday second try: After intense work, especially in the last year, this work is finally ready to be seen by the public. Led by @apramos.bsky.social and great collaboration with @carldmodes.bsky.social group especially @liormoneta.bsky.social : www.biorxiv.org/content/10.1...
The Optic cup is actively shape programmed by independently patterned apical forces
During morphogenesis, initially flat tissues often must transition into complex 3D shapes, reminiscent of shape-programmable systems in physics and engineering. One key question in developmental biolo...
www.biorxiv.org
August 22, 2025 at 2:12 PM
The Friday second try: After intense work, especially in the last year, this work is finally ready to be seen by the public. Led by @apramos.bsky.social and great collaboration with @carldmodes.bsky.social group especially @liormoneta.bsky.social : www.biorxiv.org/content/10.1...
Reposted by Martin Weigert
Our beautiful Hydra made the cover!!! 😍😍😍
An experiment performed by Pavel Mejstrik with a HCR protocol by @giuliaserafini.bsky.social, @paveltomancak.bsky.social lab @mpi-cbg.de
Actin fibers in blue, nuclei in orange.
An experiment performed by Pavel Mejstrik with a HCR protocol by @giuliaserafini.bsky.social, @paveltomancak.bsky.social lab @mpi-cbg.de
Actin fibers in blue, nuclei in orange.
August 13, 2025 at 8:51 AM
Our beautiful Hydra made the cover!!! 😍😍😍
An experiment performed by Pavel Mejstrik with a HCR protocol by @giuliaserafini.bsky.social, @paveltomancak.bsky.social lab @mpi-cbg.de
Actin fibers in blue, nuclei in orange.
An experiment performed by Pavel Mejstrik with a HCR protocol by @giuliaserafini.bsky.social, @paveltomancak.bsky.social lab @mpi-cbg.de
Actin fibers in blue, nuclei in orange.
Reposted by Martin Weigert
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/t/qupath-ext...
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 ...
forum.image.sc
August 12, 2025 at 3:10 PM
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/t/qupath-ext...
Reposted by Martin Weigert
We are today kicking off the two-week @embo.org practical course on #Lightsheet # Microscopy at @mpi-cbg.de in #Dresden. This is the fifth iteration of the course. Hashtag #LISH2025
meetings.embo.org/event/25-lsm
meetings.embo.org/event/25-lsm
Light sheet microscopy
Light sheet microscopy is a technology that enables near-isotropic imaging of large biological specimens over time. It opens new avenues to study biological processes with unprecedented imaging speed…
meetings.embo.org
August 11, 2025 at 7:49 AM
We are today kicking off the two-week @embo.org practical course on #Lightsheet # Microscopy at @mpi-cbg.de in #Dresden. This is the fifth iteration of the course. Hashtag #LISH2025
meetings.embo.org/event/25-lsm
meetings.embo.org/event/25-lsm
Reposted by Martin Weigert
Hey, it's out!
doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:
doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:
July 24, 2025 at 10:04 AM
Hey, it's out!
doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:
doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:
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
July 10, 2025 at 1:49 PM
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
Reposted by Martin Weigert
Very happy to share it’s online! If you read the preprint, updates include tracking cells and tissue flow, Histo4i timecourse (69 Abs) comparing spatial patterning emergence and a new WLS KO ipsc line establishing mechanosensing via YAP-WLS/WNT caudalizes organoids www.nature.com/articles/s41...
Morphodynamics of human early brain organoid development - Nature
Human brain morphodynamics are explored using organoids.
www.nature.com
July 1, 2025 at 8:36 PM
Very happy to share it’s online! If you read the preprint, updates include tracking cells and tissue flow, Histo4i timecourse (69 Abs) comparing spatial patterning emergence and a new WLS KO ipsc line establishing mechanosensing via YAP-WLS/WNT caudalizes organoids www.nature.com/articles/s41...
Reposted by Martin Weigert
The 2nd AI4Life Challenge is live!
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
June 27, 2025 at 1:33 PM
The 2nd AI4Life Challenge is live!
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/