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Alexander Krull @alex-krull.bsky.social · 15d

Thank you @afoix.bsky.social , thank you @virginieuhlmann.bsky.social! I am very happy and proud I was part of this one!

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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Alexander Krull @alex-krull.bsky.social · Aug 21

Cheers, for sharing, @paveltomancak.bsky.social! What a brilliant example for rotation-invariance or the lack of it.
Will go into the lecture.

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Reposted by Alexander Krull

Helmholtz Imaging @helmholtzimaging.bsky.social · Aug 18

Sept 18: Learn how to remove noise from imaging data with supervised, self-supervised & generative AI. With @alex-krull.bsky.social (University Birmingham).

Register for the series 👉 bit.ly/6-image-proc...

@helmholtz.de
#imaging #ImageDenoising #AI

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Reposted by Alexander Krull

Eric Brachmann @ericbrachmann.bsky.social · Jul 4

Looking forward to my talk at heidelberg.ai. I will touch on topics like #MapFreeReloc and #ACEZero, i.e. how to derive scene representations from very few (one!) or very many images.

cartlueth.bsky.social @cartlueth.bsky.social · Jul 4

We’re thrilled to welcome Eric Brachmann (@ericbrachmann.bsky.social‬), Senior Staff Scientist at Niantic Spatial, Inc. and a leading expert in visual relocalisation & pose estimation, to our heidelberg.ai / NCT Data Science Seminar on July 16th at 4 PM.

👇Details Below 1/3

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Alexander Krull @alex-krull.bsky.social · Jul 17

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Alexander Krull @alex-krull.bsky.social · Jul 15

Please meet Dr. @stonks1.bsky.social!
Couldn’t be more proud!

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Reposted by Alexander Krull

Florian Jug @florianjug.bsky.social · Jul 14

Submit your method to our denoising challenge!!! 👍

AI4Life @ai4life.bsky.social · Jun 27

If unsupervised approaches are your thing, also check out the unsupervised denoising challenge and submit your solutions (the challenge is from last year, but we are still taking entries from everyone who is interested).

👉 ai4life-mdc24.grand-challenge.org

AI4Life Microscopy Denoising Challenge - Grand Challenge

Wellcome to AI4Life-MDC24! In this challenge, we want to focus on an unsupervised denoising of microscopy images. By participating, researchers can contribute to a critical area of scientific research...

ai4life-mdc24.grand-challenge.org

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Reposted by Alexander Krull

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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Alexander Krull @alex-krull.bsky.social · Jul 9

Rock on, Pavel! 👍👍👍

paveltomancak.bsky.social @paveltomancak.bsky.social · Jul 9

Unlocking a cycling achievement. Koenigstuhl was like another planet for me when I was doing my PhD @embl.org. My car (old communist Škoda 105L) had trouble getting there. By bike - unthinkable. 25 years later, I did it with a bio-bike! Via #EMBL from Rohrbach. Next challenge: #Steigerweg 🤠💪🚴‍♀️

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Reposted by Alexander Krull

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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Reposted by Alexander Krull

Florian Jug @florianjug.bsky.social · Jun 30

Join the challenge, get the data, contribute your solution!!! 🎉

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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Alexander Krull @alex-krull.bsky.social · Jun 10

The submission for 2025's BioImage Computing @iccv.bsky.social is now open. If things go like the last years, I am looking forward to all you brilliant submissions.
www.bioimagecomputing.com

BioImage Computing

a truly interdisciplinary workshop

www.bioimagecomputing.com

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Alexander Krull @alex-krull.bsky.social · Jun 6

Congrats, guys!

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Reposted by Alexander Krull

Constantin Pape @cppape.bsky.social · Feb 12

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...

Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.

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Reposted by Alexander Krull

Peyman Milanfar @docmilanfar.bsky.social · Mar 18

Tweedie's formula is super important in diffusion models & is also one of the cornerstones of empirical Bayes methods.

Given how easy it is to derive, it's surprising how recently it was discovered ('50s). It was published a while later when Tweedie wrote Stein about it

1/n

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Reposted by Alexander Krull

Moritz Bartl @kommunikationsliebe.org · Mar 13

"Having trouble selling your #tesla? Tired of being associated with a toxic, Nazi-adjacent brand? We understand that there’s a shrinking market of buyers and limited selling options for current owners.

Our experienced team specializes in discreetly acquiring and transporting your car to […]

Original post on social.tchncs.de

social.tchncs.de

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Alexander Krull @alex-krull.bsky.social · Mar 13

Wow! Congrats!

Constantin Pape @cppape.bsky.social · Mar 13

Segment Anything for Microscopy made the cover! Check out the amazing artwork by Sebastian:

Sebastian von Haaren @haarensv.bsky.social · Mar 13

A small but special moment: My illustration is on the cover of the March issue of Nature Methods!

A huge hug to @anwaiarchit.bsky.social and @cppape.bsky.social — it was a pleasure to work alongside you on this!

www.nature.com/nmeth/volume...

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Alexander Krull @alex-krull.bsky.social · Mar 4

@docmilanfar.bsky.social , love this. Max likelihood points to x. This refers to the fact that the noisy data x is actually the max likelihood est. of u?

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Reposted by Alexander Krull

Peyman Milanfar @docmilanfar.bsky.social · Mar 4

Have you said thank you once to Tweedie?

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Florian Jug @florianjug.bsky.social · Feb 24

🚨 Fantastic opportunity to conduct a PhD in Europe! European funding and fantastic international community! 👩‍🎓

Alexandre Benmerah @alexbnmrh.bsky.social · Jan 13

14 PhD Positions in the Cilia-AI Consortium!

Cilia-AI is a European training rogramme for deconvolution of multi-scale cilia function in health and disease by integrating machine learning-AI approaches.

www.cilia-ai.eu

Cilia-AI

www.cilia-ai.eu

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Reposted by Alexander Krull

Theory of Living Matter Group @tlmcambridge.bsky.social · Feb 27

🚨Next week, Wed 05/03 | 16:00 UK - Online Seminar🚨

"Turning morphology into numbers across microscopy scales and modalities" by Dr Virginie Uhlmann.

To attend online please register to our 📧 for the zoom link: lists.cam.ac.uk/sympa/subscr...

Poster for Theory of Living Matter seminar series talk 05 March 2025 at 16:00 UK time. Speaker is Virginie Uhlmann from BioVisionCenter, University of Zurich and EMBL-EBI. The talk is entitled "Turning morphology into numbers across microscopy scales and modalities", with the following abstract: Microscopy image data constitute the primary source of observational data on living systems across scales, and recent advances in microscopy technologies now enable the multi-modal observation of identical biological specimen. A key question emerges from this abundance of image data: how can we consistently quantify what we see? This endeavour is particularly complex for morphology, which involves intricate combinations of visual features that appear fundamentally different across various imaging modalities. Motivated by this challenge, my research group has been focusing on abstracting the problem of image-based morphology quantification from specific imaging modalities. In this seminar, I will present how we are building bits by bits the computational tools needed to extract modality-agnostic shape descriptors from microscopy images, how we use them to investigate fundamental biological questions, and what are the promising directions we are pursuing towards establishing a general framework to quantify biological morphology across imaging modalities.

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Reposted by Alexander Krull

Uni Göttingen @uni-goettingen.de · Feb 26

Automatische Zellanalyse mit #KI: Forschende trainierten eine bestehende, KI-basierte Software neu. Das Modell „Segment Anything for Microscopy“ kann Bilder von Geweben, Zellen und anderen Strukturen genau segmentieren: s.gwdg.de/HqkMz2; s.gwdg.de/iTejKW

Forschungsteam mit bsky.app/profile/cppa...

Pflanzenzellen, die mit einem Fluoreszenzmikroskop aufgenommen und mit dem Modell automatisch segmentiert wurden. Die zugrunde liegenden Daten sind dreidimensional und das Bild zeigt eine Darstellung der segmentierten Zellen, die jeweils durch eine andere Farbe repräsentiert werden.

Foto: Nature Methods: 10.1038/s41592-024-02580-4

Segmentierung von Zellen in der Lichtmikroskopie mit μSAM. Das Bild zeigt, wie Zellen in der Phasenkontrastmikroskopie mit μSAM segmentiert werden können. Grüne Punkte und Kästchen zeigen die Benutzereingabe und farbige Masken die entsprechende Vorhersage des Modells.

Foto: Erstellt von Anwai Archit mit dem μSAM-Tool, verfügbar in Nature Methods: 10.1038/s41592-024-02580-4

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Alexander Krull @alex-krull.bsky.social · Feb 25

Loved it!

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Reposted by Alexander Krull

Florian Jug @florianjug.bsky.social · Feb 17

Amaaazing bunch of students, TAs, and faculty come together for this! Thank you all for joining us here this week! #EMBLDeepLearning

Anna @ilastik-team.bsky.social Kreshuk, @maweigert.bsky.social, @cppape.bsky.social, @alex-krull.bsky.social, @janfunkey.bsky.social, and many more… ❤️

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Reposted by Alexander Krull

Florian Jug @florianjug.bsky.social · Feb 17

‼️🔬 We start!!! 🎉🤖
Super exciting!!! After years of teaching courses for #DeepLearning for Microscopy and Life Science application, we start today our first “advanced course” @embl.org!
#EMBLDeepLearning

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