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Matthias Meyer-Bender

@matthiasmeybe.bsky.social
79 followers 71 following 7 posts

PhD student at EMBL Heidelberg Interested in computational biology, biological image analysis and AI in medicine

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Reposted by Matthias Meyer-Bender
Wolfgang Huber @wkhuber.bsky.social · 28/07/2026
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data By @matthiasmeybe.bsky.social et al. Great collaboration with the group of Sascha Dietrich and Peter-Martin Bruch. doi.org/10.1038/s415...
multiplexed immunohistochemistry of lymphoma biopsies, arranged as a hexagon
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Reposted by Matthias Meyer-Bender
EMBL @embl.org · 28/07/2026
EMBL and collaborators have developed spatialproteomics, an open-source package that helps researchers analyse how cells are organised within tumours. In lymphoma samples, it revealed spatial patterns that distinguish indolent from aggressive entities. www.embl.org/news/science...
embl.org
New software helps researchers decode the cellular architecture of lymphoma | EMBL
EMBL scientists and collaborators developed spatialproteomics, an open-source tool that helps researchers analyse how cells are organised within tumours.
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Matthias Meyer-Bender @matthiasmeybe.bsky.social · 24/07/2026
🚀 Our paper on spatialproteomics is now out in @natmethods.nature.com Spatialproteomics is a Python package for analyzing highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem. www.nature.com/articles/s41...
Spatialproteomics is a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem.
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Reposted by Matthias Meyer-Bender
Nav @naveed-ishaque.bsky.social · 18/06/2026
Cell segmentation for spatial transcriptomics isn’t so easy, right? We thought so too. A wonderful group lead by @garybader.bsky.social and @rgottardo.bsky.social put together a perspectives piece on where things stand, the challenges, and what’s next. Check it out: arxiv.org/pdf/2606.09675
arxiv.org
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Reposted by Matthias Meyer-Bender
Wolfgang Huber @wkhuber.bsky.social · 29/05/2026
Thanks to input from @helucro.bsky.social, Daria Lazic, Hugo Gruson, Artür Manukyan and many others, there is now a whole new level of maturity and ease-of-use for spatial omics data, see helenalc.github.io/SpatialData....
helenalc.github.io
csama – SpatialData
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Reposted by Matthias Meyer-Bender
EMBL-EBI Training @training.ebi.embl.org · 16/02/2026
Join us next week for the second free webinar in our spatial transcriptomics series: www.ebi.ac.uk/training/eve... Daria Lazic (EMBL Heidelberg) presents 'Imaging-based spatial transcriptomics: methods, preprocessing, and quality control' on 25 February | 14:30 UK time.
Webinar at EMBL-EBI: "Imaging-based spatial transcriptomics: methods, preprocessing, and quality control". 25-02-2026, 14:30-15:30 GMT. Speaker (with photo): Daria Lazic, EMBL Heidelberg
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Reposted by Matthias Meyer-Bender
Luca Marconato @lucamarconato.bsky.social · 02/02/2026
We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework. We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community. 🔗 Deadline: 15/02/2026 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
embl.wd103.myworkdayjobs.com
Research Software Engineer - Spatial-omics
The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...
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Reposted by Matthias Meyer-Bender
EMBL @embl.org · 26/01/2026
Recruitment for the EMBL International PhD Programme is officially open! 🔊 At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us! 🔎 Read more here: tinyurl.com/4jdt2ra5
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Reposted by Matthias Meyer-Bender
Python Software Foundation @python.org · 27/10/2025
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-... 🧵
python.org
The official home of the Python Programming Language
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Reposted by Matthias Meyer-Bender
Jonas Schiller @jonas-bio.bsky.social · 15/10/2025
Latitudinal diversity gradients (LDGs) are found across 🌱🐨🦠 but their underlying mechanisms remain unclear. In this study, we highlight that LDGs are not universal in marine microbiomes but reflect lineage-specific ecological strategies and environmental responses. doi.org/10.1101/2025...
doi.org
Variations in the latitudinal diversity gradients of the ocean microbiome
Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...
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Reposted by Matthias Meyer-Bender
Wolfgang Huber @wkhuber.bsky.social · 04/10/2025
(Huber lab)[EMBL] welcomes applications for a PhD in ML for spatial omics [representation learning + integration with biostatistics, cell + anatomy foundation models, collaborate with domain scientists on cancer and dev:bio discovery science] |> Apply though the ELLIS portal ::: Deadline 2025-10-31
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Reposted by Matthias Meyer-Bender
Anna Foix @afoix.bsky.social · 23/09/2025
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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Reposted by Matthias Meyer-Bender
EMBL @embl.org · 22/09/2025
EMBL International PhD Programme - winter recruitment 2026! 📣 Research groups across EMBL are recruiting now! www.embl.org/about/info/e... Don’t miss this opportunity to receive dedicated mentoring while doing interdisciplinary research.
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Reposted by Matthias Meyer-Bender
Martin Emons @martinemons.bsky.social · 11/09/2025
We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data academic.oup.com/nar/article/...
academic.oup.com
Harnessing the potential of spatial statistics for spatial omics data with pasta
Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba
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Reposted by Matthias Meyer-Bender
Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
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Reposted by Matthias Meyer-Bender
Martin Emons @martinemons.bsky.social · 27/06/2025
Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”. We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases. arxiv.org/abs/2412.01561
arxiv.org
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
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Reposted by Matthias Meyer-Bender
Leonie Lorenz @leonielorenz.bsky.social · 07/05/2025
Very happy and proud to announce that the first preprint of my PhD is out: arxiv.org/abs/2504.20710 We developed an R package to translate mathematical models in SBML format into executable odin models and visualise models from @biomodels.bsky.social on our website Menelmacar biomodels.bacpop.org
arxiv.org
SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computati...
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Matthias Meyer-Bender @matthiasmeybe.bsky.social · 05/05/2025
New preprint out! We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem. www.biorxiv.org/content/10.1...
Spatialproteomics orchestrates workflows to analyze highly multiplexed images. It segments cells, processes images, quantifies proteins, predicts cell types, and provides neighborhood analysis methods, all while integrating into the scverse ecosystem.
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Reposted by Matthias Meyer-Bender
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 04/05/2025
Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data www.biorxiv.org/content/10.1101/202…
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Reposted by Matthias Meyer-Bender
Wolfgang Huber @wkhuber.bsky.social · 12/03/2025
Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data www.huber.embl.de/group/posts/...
huber.embl.de
Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data – Huber Group @ EMBL
Precision Oncology and Multiomics
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Reposted by Matthias Meyer-Bender
Wolfgang Huber @wkhuber.bsky.social · 03/10/2023
*Medical Data Scientist Postdoc* Program by Medical Faculty Uni Heidelberg. Join S.Dietrich, J.Lu & me to work on statistical& AI methods applied to single cell and spatial omics to improve immunotherapies: www.medizinische-fakultaet-hd.uni-heidelberg.de/forschung/fo... www.embl.org/about/info/m...
medizinische-fakultaet-hd.uni-heidelberg.de
Medizinische Fakultät Heidelberg: Medical Data Scientist Programm
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