carsten marr
@MarrCarsten
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Analyzing and modeling single cells in biomedical data
Helmholtz Munich, GER
Joined June 2018
Introducing HistoGPT: A Foundation Model for AI-Powered Pathology Reports. 💡A new AI tool with the potential to transform dermatopathology by automating process of generating high-quality pathology reports from histology images. 🔗 https://t.co/6EsK9atwhE
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Great collaboration and great model design from @ValentinKoch_ !
5/ Cool work together w/ Sabine Bauer from Heart Centre Munich, thanks to co-authors and advisors @VLupperger, Michael Joner, Heribert Schunkert, @ja_schnabel, Moritz von Scheidt and @MarrCarsten! preprint: https://t.co/UWO1hmRFpC 🤑 code: https://t.co/CJMow09fXd 🤓
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Proud of the first chapter, hopefully of many, of our collaboration with @JungmannLab published in @CellCellPress where SUM-PAINT was developed for imaging neurons. Kudos to Eduard Unterauer @jekriste @mahipal_ganji @l_masu @MarrCarsten @FelipeOpaz_o. https://t.co/Dvmy9KxSQ4
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Difference in Piezo1-dependent Ca2+-influx, so what? To show "what", we teamed up with @MarrCarsten's lab, adopting their custom-developed RBC morphology analysis algorithm. Ca2+-influx causes K+-efflux and loss of water from RBC - cells shrink. 8/n
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Amazing collaboration indeed with generous funding from @VolkswagenSt
Happy to share the outcome of a long-standing collaboration with @DrukkerMicha and @MarrCarsten on mechanisms of species-specific differentiation speed https://t.co/ID5wJd2wJN
@mpimoph @HelmholtzMunich @LACDR A thread
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Our innovation grant-winning study on AI-based OCT analysis post-PCI is on medRxiv! DeepNeo is a tool for neointima & stent analysis with a GUI (⬇️) ! It classifies neoint. w same acc as experts + strong segmentation of lumen, stent and neoint.🔬 1/6 https://t.co/AfjwaG3RC9
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#PositionPaper 🇩🇪 Experts offers solutions to navigate the complexities of using #patient #data in #medical #research, addressing privacy concerns while maximizing #AI's potential. 👉Read more about their recommendations https://t.co/4JXpJ3HKU8
#HelmholtzMunich @MarrCarsten
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Amazing work from @ValentinKoch_ and @sophiajwagner !!! Thank you both!
Excited to introduce DinoBloom🦖🌺, an open-source foundation model family (Vit-S to G) for general cell embeddings in #hematology🩸 Trained w mod. #DINOv2 on 13 datasets w 380,000+ WBC images of blood & bonemarrow. Evaluated on AML subtype & cell classification (knn, lin probe)
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... how could I forget to tag @sophiajwagner (Hope you enjoy your research visit @AI4Pathology !) and Robert from @laion_ai (also in US right now?) ? Best regards from Munich!
I am thrilled to announce HistoGPT, a vision language foundation model that generates highly accurate pathology reports from gigapixel whole slide images. medRxiv: https://t.co/63e8qmNRZj GitHub: https://t.co/H8tLifsqtA Hugging Face: https://t.co/7YrFLZ97mQ
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I am thrilled to announce HistoGPT, a vision language foundation model that generates highly accurate pathology reports from gigapixel whole slide images. medRxiv: https://t.co/63e8qmNRZj GitHub: https://t.co/H8tLifsqtA Hugging Face: https://t.co/7YrFLZ97mQ
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🎉 Stoked that @ErnstRoell's first Ph.D. work "Differentiable Euler Characteristic Transforms for Shape Classification" was accepted @iclr_conf #ICLR2024 👉A new, super fast topological layer (based on Euler Characteristic Transform) #geometry #topology #MachineLearning 🧵1/n
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🎉@iclr_conf: Simplicial Representation Learning w/ Neural k-Forms #Geometry #MachineLearning #ICLR2024 📜 https://t.co/5Y2KPsCMHk TL;DR: Learnable differential forms = ꜰᴇᴀᴛᴜʀᴇ ᴍᴀᴘꜱ for combinatorial complexes (like graphs), enabling classification + more! 🧵1/n
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My new lab at the Institute of AI for Health at @HelmholtzMunich is looking for postdocs! Great projects in AI for discovery of antimicrobial peptides and Computational oncology. RT or apply!
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Great projects, great environment, great supervisor ;-). Pls share / apply!
To future PhD students! My lab offers two super exciting positions to work on AI-driven antimicrobial peptide discovery. Please share and apply. Can't wait to work on this topic with you☺️! Both positions are funded by @ERC_Research. Check the ad here:
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Interested in #Foundation #Models in #Health / #Medicine? -> Consider stopping by: April 10, @HelmholtzMunich 3 #keynotes, an exciting scientific program, and networking opportunities await. Registration / abstract submission: https://t.co/BoRrI54Qy0
@fabian_theis @MarrCarsten
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Takeaways: - finetuning can be achieved with low resources (we used 1 GPU only + batch size 32 was sufficient for training ViT-g) - even for small datasets finetuning strong CV foundation models might be better than histo-pre-trained feature extractors 3/
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⚡️Want to save compute when training your feature extractor for histopathology?🔬💻#CPath Study on 1(!) GPU for 2 CRC tasks led by our fantastic master student @roth_benedikt13, co-supervised with @ValentinKoch_ pre-print: https://t.co/J73f7sGmDy code: https://t.co/jRN3IV6CdE 1/
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Check out the new promo video of my PhD program 📹👇🏼 Congratulations #EpiCrossBorders! 🇩🇪🏴 @epigeneticsHMGU @HelmholtzMunich @EdinburghUni
Learn more about EpiCrossBorders ! Video featuring our #Epigentics focused international PhD program -joint btw. @HelmholtzMunich and @EdinburghUni - is now online . 👁️ and share: https://t.co/vd0ifQxHZK
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📢 Our (@KazeminiaSalome, @MarrCarsten) paper on topologically regularized multiple instance learning (MIL) for rare anemia disorder classification is on arXiv! https://t.co/ymErAPeGVu 1/8
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Congrats Scott and @dominik_waibel for this feat!!! A truly inspiring interdisciplinary work with @Meier_Lab between @PioneerCampus and @CompHealthMuc at @HelmholtzMunich
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