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Mann Lab

@mannlab.bsky.social

640 followers 1 following 96 posts

The Mann Lab is a pioneer in mass spectrometry-based proteomics. Posts represent personal views from lab members and Matthias Mann

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Mann Lab @mannlab.bsky.social · Jul 1

Thank you Matthias for your visionary leadership and for creating a scientific family that continues to push boundaries. Congratulations from all members, and looking forward to the future! #MS #Proteomics #20Years

Max Planck Institute of Biochemistry @mpibiochem.bsky.social · Jul 1

🎉 Congratulations to Matthias Mann on 20 years leading Proteomics & Signal Transduction at MPI of Biochemistry! Two decades of groundbreaking mass spectrometry research and training excellent future scientists.

#MS #Proteomics #Science @mannlab.bsky.social

Mann Lab @mannlab.bsky.social · 14d

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If this interests you:
🔁 Retweet the first post:
bsky.app/profile/mann...
⭐️ Give our github repo a star github.com/MannLabs/scP...
❓ tell us what you are going to do with #scPortrait

Mann Lab @mannlab.bsky.social · 14d

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This work was a fantastic collaboration:
@mannlab.bsky.social
@fabiantheis.bsky.social
@v-hornung.bsky.social
A big shoutout to all of our co-authors: Alessandro Palma,
Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova, Mahima Arunkumar, @lukasheumos.bsky.social, @georgwa.bsky.social

Mann Lab @mannlab.bsky.social · 14d

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Bottom line:
scPortrait turns microscopy images into a first-class modality for machine learning and multimodal foundation models, alongside RNA and proteomics 🔬💻
🔗 Preprint: doi.org/10.1101/2025...
🔗 GitHub: github.com/MannLabs/scP...

scPortrait integrates single-cell images into multimodal modeling

Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are accessi...

Mann Lab @mannlab.bsky.social · 14d

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Our extensive documentation and tutorials make scPortrait easy to use and accessible.
And as part of @scverse.bsky.social it’s compatible with existing tools like scanpy, squidpy, bento-tools or Moscot 🚀🐍
mannlabs.github.io/scPortrait/i... #OpenSourceTools #Tutorial #CodeDocumentation

Mann Lab @mannlab.bsky.social · 14d

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scPortrait already scales:
1️⃣ 120M+ single-cell images from image-based genetic screens
2️⃣ applied on patient-derived datasets to perform AI-driven morphology analysis
Refs:
1️⃣ BioRxiv2023 ➡️ www.biorxiv.org/content/10.1...
2️⃣ Nature 2025➡️ www.nature.com/articles/s41...

SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes

Forward genetic screening associates phenotypes with genotypes by randomly inducing mutations and then identifying those that result in phenotypic changes of interest. Here we present spatially resolv...

www.biorxiv.org

Mann Lab @mannlab.bsky.social · 14d

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We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler

Mann Lab @mannlab.bsky.social · 14d

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✨ Embedding images into transcriptome atlases ✨
We use scPortrait to embed single-cell images from a @10xgenomics.bsky.social Xenium ovarian cancer dataset into the #SCimilarity transcriptome atlas (R2 = 0.65), recovering meaningful cell types

Mann Lab @mannlab.bsky.social · 14d

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✨ Morphology defined cell states ✨
Image embeddings generated with scPortrait resolve intra- vs extratumoral macrophages with distinct morphologies, linked to anti-inflammatory vs fibroblast-like programs

Mann Lab @mannlab.bsky.social · 14d

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✨ Transcriptomes from images ✨
Using optimal transport + flow matching, scPortrait generates gene expression directly from CODEX images, capturing canonical marker expression like TCL1A in germinal centers in the tonsil
#CODEX #flowmatching #OT

Mann Lab @mannlab.bsky.social · 14d

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With standardized single-cell image datasets in place, the key question is: what new biology can we unlock?
We highlight three use-cases for scPortrait

Mann Lab @mannlab.bsky.social · 14d

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The new .h5sc format provides fast random access to single-cell images for ML training.
It follows #FAIR data principles (findable, accessible, interoperable, reusable) and integrates with @scverse.bsky.social tools via AnnData.

Mann Lab @mannlab.bsky.social · 14d

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The scPortrait pipeline transforms raw input images step by step:
• stitch FOVs
• segment & extract cells
• output standardized .h5sc single-cell image datasets

From messy pixels → inputs ready for training 🖥️

Mann Lab @mannlab.bsky.social · 14d

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Problem: microscopy images are messy, fragmented, and hard to use for ML
Solution: scPortrait standardizes them into a new .h5sc single-cell image format turning 🔬microscopy images into a reusable resource for integrative cell modeling

Mann Lab @mannlab.bsky.social · 14d

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Microscopy images are:
📈 easy to acquire across scales (organism → subcellular)
🖥️ information-rich (cellular architecture, tissue structure, perturbation responses)
= 🚀 ideal fuel for foundation models of cell behavior

Mann Lab @mannlab.bsky.social · 14d

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AI has had major breakthroughs (#alphafold #chatgpt) & computational models can now detect patterns in complex datasets without external guidance 🧠🖥️

🧬 biological datasets often contain entangled information making them complex to interpret →🧠🖥️ + 🧬 = unlock new biology

Mann Lab @mannlab.bsky.social · 14d

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Tomorrow’s large scale cross-modality models will further unlock biology, but they need standardized inputs. With @sophia-maedler.bsky.social & @nik-as.bsky.social, we built #scPortrait, @scverse.bsky.social package to turn microscopy images into single-cell image datasets for multimodal modeling

Mann Lab @mannlab.bsky.social · 14d

Our preprint on scPortrait is out! We built a framework + format to turn microscopy into standardized single-cell image datasets. #scPortrait scales >100M cells, integrates with @scverse.bsky.social, & enables cross-modality modeling from morphology to transcriptomics
doi.org/10.1101/2025...

scPortrait integrates single-cell images into multimodal modeling

Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are accessi...

Mann Lab @mannlab.bsky.social · 23d

Congratulations on the inaugural of #AITHYRA, the new Biomedical AI institute in Vienna. Thank you for the invitation to speak at the symposium and the fascinating discussions on AI × proteomics. #AIforLifeScience

Mann Lab @mannlab.bsky.social · 28d

Thanks CPR, reNEW, @ucph.bsky.social
Full story:
www.sciencedirect.com/science/arti...

Mann Lab @mannlab.bsky.social · 28d

Withdrawal of the stem-cell niche WNR (Wnt-Noggin-R-spondin) cocktail in organoid cultures decreased proliferation and stemness, as well as improved differentiation, moving organoids toward more tissue-like states.

Mann Lab @mannlab.bsky.social · 28d

scDVP’s high-resolution enabled us to observe fine-grained protein abundance changes along the colon crypt axis. For instance, the abundance gradient of CA1 was only visible in organoid transplants and in vivo tissue.

Mann Lab @mannlab.bsky.social · 28d

We further employed scDVP to explore differences in individual intestinal epithelial cells. This dataset comprised about 2,700 proteins across cell types, and confirmed clearer stemness-to-differentiation programs after organoid xenotransplantation.

Mann Lab @mannlab.bsky.social · 28d

Led by @freddyomics.bsky.social‬ and @hausmannannika.bsky.social‬, we created a spatial human colon resource consisting of almost 8,000 protein groups across distinct cell types! This reference enabled us to assess cell populations of human colon organoids and establish a colon stemness signature.

Mann Lab @mannlab.bsky.social · 28d

Out in @cp-cellsystems.bsky.social‬: Deep Visual Proteomics shows xenotransplantation drives colon #organoids toward in-vivo-like proteomes supporting their use in regenerative medicine; culture tweaks can mimic this shift. With @kimbakjensen.bsky.social. Lead author Frederik Post explains below:

Mann Lab @mannlab.bsky.social · Sep 1

If you are interested in scientific software engineering or experimental work in the fields of spatial and multi-modal -omics, high throughput interaction proteomics, or mass instrumentation, apply until Oct 7th! @mannlab.bsky.social
www.biochem.mpg.de/mann
imprs-ml.mpg.de/How-to-Apply

Learn more about our application process

imprs-ml.mpg.de