maweigert.bsky.social
Martin Weigert
@maweigert.bsky.social
960 followers 210 following 11 posts
Machine Learning for Microscopy | Prof @ TU Dresden | https://scholar.google.com/citations?user=ZltxyqoAAAAJ
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maweigert.bsky.social
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
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afoix.bsky.social
Anna Foix @afoix.bsky.social · 15d
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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kuba-sedzinski.bsky.social
kuba sędziński @kuba-sedzinski.bsky.social · 16d
🧵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
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aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 19d
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
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cryaaa.bsky.social
Ryan Savill @cryaaa.bsky.social · 26d
(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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vmsruetten.bsky.social
Virginia M. S. Ruetten @vmsruetten.bsky.social · Sep 8
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.
mishaahrens.bsky.social
Misha Ahrens @mishaahrens.bsky.social · Sep 8
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...
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ekatrukha.bsky.social
Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · Sep 5
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)
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nature.com
Nature @nature.com · Sep 3
How is this possible?

This ant can lay eggs of two different species, birthed by the same mother
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maweigert.bsky.social
Martin Weigert @maweigert.bsky.social · Sep 4
Congrats!! Way to go Akanksha!
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akanksha-jain.bsky.social
Jain_Akanksha_ @akanksha-jain.bsky.social · Sep 3
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 🧠🔬🧬
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mpi-cbg.de
Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · Sep 3
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
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icepfl.bsky.social
EPFL School of Computer and Communication Sciences @icepfl.bsky.social · Sep 2
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...
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giodang.bsky.social
Giovanni D’Angelo @giodang.bsky.social · Sep 3
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
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
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nadlerlab.bsky.social
André Nadler @nadlerlab.bsky.social · Aug 21
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...
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hhmijanelia.bsky.social
Janelia Research Campus @hhmijanelia.bsky.social · Aug 26
📢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
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kyleharrington.com
Kyle Harrington @kyleharrington.com · Aug 26
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...
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
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loicaroyer.bsky.social
Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · Aug 25
🧬🔬🧪 🎉 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...
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nordenlab.bsky.social
NordenLab @nordenlab.bsky.social · Aug 22
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
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anaisbailles.bsky.social
Anaïs Bailles @anaisbailles.bsky.social · Aug 13
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.
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nkiaru.bsky.social
Nicolas Chiaruttini @nkiaru.bsky.social · Aug 12
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3)

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
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paveltomancak.bsky.social
paveltomancak.bsky.social @paveltomancak.bsky.social · Aug 11
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
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
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nkiaru.bsky.social
Nicolas Chiaruttini @nkiaru.bsky.social · Jul 24
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:
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maweigert.bsky.social
Martin Weigert @maweigert.bsky.social · Jul 10
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
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akanksha-jain.bsky.social
Jain_Akanksha_ @akanksha-jain.bsky.social · Jul 1
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
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ai4life.bsky.social
AI4Life @ai4life.bsky.social · Jun 27
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/
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nature.com
Nature @nature.com · Jun 24
Nature research paper: Morphodynamics of human early brain organoid development

https://go.nature.com/4l7fDmc
Morphodynamics of human early brain organoid development - Nature
Human brain morphodynamics are explored using organoids.
go.nature.com
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