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JungmannLab @jungmannlab.bsky.social · 11/03/2026

We hope G5M pushes molecular mapping forward. Excited to see the discoveries it enables! Thanks to @rafalkowalew.bsky.social, @susannereinhardt.bsky.social, @ipachmayr.bsky.social, Shuhan Xu, @lumasullo.bsky.social for developing G5M and the @jungmannlab.bsky.social for testing and improving it. 7/7

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JungmannLab @jungmannlab.bsky.social · 11/03/2026

G5M is implemented in Picasso since version 0.9.5: github.com/jungmannlab/..., although we always recommend using the most recent version! A short documentation: picassosr.readthedocs.io/en/latest/re.... We advise reading the whole paper for best results! 6/7

github.com

GitHub - jungmannlab/picasso: A collection of tools for painting super-resolution images

A collection of tools for painting super-resolution images - jungmannlab/picasso

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JungmannLab @jungmannlab.bsky.social · 11/03/2026

Bonus: we found a new formula for axial loc. precision for astigmatic imaging for any z position. It only depends on the 3D calibration and the properties of localizations. Interestingly, the results are not necessarily symmetric around z = 0. 5/7

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JungmannLab @jungmannlab.bsky.social · 11/03/2026

We validated G5M on DNA origami, Nuclear Pore Complexes (NPCs) and Obinutuzumab-treated CD20 RESI data. In NPCs, G5M found twice as many Nup96 dimers as GA, demonstrating increased accuracy in molecular mapping. 4/7

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JungmannLab @jungmannlab.bsky.social · 11/03/2026

G5M uses modified Gaussian mixture modeling to accurately capture the shape of 2D and 3D astigmatic localization clouds. In realistic simulations, it resolves molecules spaced 2.9 localization precisions apart with a 27× higher recovery rate than other tools. 3/7

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JungmannLab @jungmannlab.bsky.social · 11/03/2026

Knowing where biomolecules are is key to uncovering molecular interactions and patterns. But standard clustering methods (e.g., DBSCAN, GA) often fail when proteins are spaced <5× the localization precision, leading to false negatives and misassignments. 2/7

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JungmannLab @jungmannlab.bsky.social · 07/02/2026

Big congrats to Clemens Steinek, @ipachmayr.bsky.social, and Sebastian Strauss who led the project as well as other co-authors that contributed to this work!! 6/6

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JungmannLab @jungmannlab.bsky.social · 07/02/2026

Importantly, this workflow is broadly applicable and compatible with virtually any high off-rate binder. Many “bad” binders currently sitting in lab freezers may now become powerful imaging tools. 5/6

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JungmannLab @jungmannlab.bsky.social · 07/02/2026

Using DyBE, we resolved the organization of receptor tyrosine kinases at single-protein resolution and detected ligand-dependent homodimerization of HER2, as well as EGF-induced formation of EGFR homodimers and EGFR–HER2 heterodimers. 4/6

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JungmannLab @jungmannlab.bsky.social · 07/02/2026

DyBE increases protein labeling up to 15-fold for high off-rate nanobodies, enabling visualization of most molecules of a given target protein within the cell. 3/6

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JungmannLab @jungmannlab.bsky.social · 07/02/2026

In classical DNA-PAINT, small binders such as nanobodies can localize proteins with nanometer precision, but rapid unbinding often limits efficient protein labeling. DyBE adapts DNA-PAINT to harness small, high off-rate binders for nanometer-precise sampling. 2/6

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JungmannLab @jungmannlab.bsky.social · 07/02/2026

Here we introduce Dynamic Binder Exchange (DyBE), a new strategy that uses the high off-rate kinetics of small binders to map proteins with nanometer-scale precision! 1/6

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Philipp Steen @philippsteen.bsky.social · 26/01/2026

How do you scale super-resolution microscopy to dozens of proteins without linearly scaling imaging time? We introduce Combi-PAINT: a combinatorial DNA-PAINT strategy that breaks the 1-target-per-round bottleneck of Exchange-PAINT: www.biorxiv.org/content/10.6... 1/5

biorxiv.org

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SPIE @spie.org · 18/01/2026

Ralf Jungmann, of the @mpibiochem.bsky.social, is the first speaker to step to the BiOS Hot Topics stage at #PhotonicsWest!💡 He is delivering his presentation titled: “From DNA nanotechnology to biomedical insight: towards single-molecule spatial omics” @jungmannlab.bsky.social

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Nature Nanotechnology @natnano.nature.com · 17/10/2025

Now online: October 2025 Issue. - Focus Issue on #biosensing, - DNA moiré superlattices, - Sugars at Ångström-resolution, - Solid-state #nanopores, - Non-aqueous Li #batteries, - - Neuromorphic vision, - Peptide #hydrogels, - Deep learning for #LNPs and more... www.nature.com/nnano/volume...

The image on the cover shows two sugars from the same cell-surface glycan separated by 9 Å, visualized with RESI (resolution enhancement by sequential imaging) enabled by metabolic labelling with DNA barcodes.

IMAGE: Luciano A. Masullo, Max Planck Institute of Biochemistry, Germany.

COVER DESIGN: Vanitha Selvarajan

Original paper: Masullo, L.A., et al. Ångström-resolution imaging of cell-surface glycans. Nat. Nanotechnol. 20, 1457–1463 (2025). https://doi.org/10.1038/s41565-025-01966-5

Abstract: Glycobiology is rooted in the study of monosaccharides, ångström-sized molecules that are the building blocks of glycosylation. Glycosylated biomolecules form the glycocalyx, a dense coat encasing every human cell with central relevance—among others—in immunology, oncology and virology. To understand glycosylation function, visualizing its molecular structure is fundamental. However, the ability to visualize the molecular architecture of the glycocalyx has remained challenging. Techniques such as mass spectrometry, electron microscopy and fluorescence microscopy lack the necessary cellular context, specificity and resolution. Here we combine resolution enhancement by sequential imaging with metabolic labelling, enabling the visualization of individual sugars within glycans on the cell surface, thus obtaining images of the glycocalyx with a spatial resolution down to 9 Å in an optical microscope.

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JungmannLab @jungmannlab.bsky.social · 02/10/2025

Within this neuronal atlas we can reveal the three synapse classes, excitatory, inhibitory and the recently discovered mixed synapse. Organelle imaging of Peroxisomes (Pmp70) and the Golgi Apparatus (Golga5) reveals rare contact sides and even fused particles. (5/6)

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JungmannLab @jungmannlab.bsky.social · 02/10/2025

To show the power of the technique, we acquired a 13-plex 200 x 200 µm2 neuronal atlas in 3D. With this atlas we map the interaction architecture of three neurons, resolving organelles, cytoskeleton, vesicles and synapses at single-protein resolution. (4/6)

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JungmannLab @jungmannlab.bsky.social · 02/10/2025

We demonstrate speed-optimized left-handed DNA-PAINT by characterizing the sequence binding kinetics and resolving three main microscopy benchmarking targets, mitochondria, microtubules and nuclear pore complexes with <5 nm localization precision. (3/6)

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JungmannLab @jungmannlab.bsky.social · 02/10/2025

The mirrored design of left-handed oligonucleotides allows the extension of the common 6 speed-sequences R1-R6 with their analogs L1-L6, enabling 12 target multiplexing with a standard secondary label-free DNA-PAINT workflow. (2/6)

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JungmannLab @jungmannlab.bsky.social · 02/10/2025

Highly efficient 12-color multiplexing with speed-optimized DNA-PAINT. We are excited to share our latest paper in @natcomms.nature.com, using left-handed DNA to extend speed-optimized DNA-PAINT to 12 targets in a simple and straightforward way! 🧬👈🚀https://www.nature.com/articles/s41467-025-64228-x

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Heilemann Lab @heilemannlab.bsky.social · 27/08/2025

Next on stage is Eduard Unterauer @eduardunterauer.bsky.social from @jungmannlab.bsky.social reporting spatial proteomics with DNA PAINT #SMLMS2025

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Nature Nanotechnology @natnano.nature.com · 28/07/2025

New paper online: Ångström-resolution imaging of cell-surface glycans. The molecular organization of sugars in the native #glycocalyx has been resolved at 9 ångström using bioorthogonal metabolic labeling and #superresolution imaging of DNA barcodes. #Glycotime www.nature.com/articles/s41...

nature.com

Ångström-resolution imaging of cell-surface glycans - Nature Nanotechnology

By combining bioorthogonal metabolic labelling and resolution enhancement through sequential imaging of DNA barcodes, the molecular organization of individual sugars in the native glycocalyx has been ...

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JungmannLab @jungmannlab.bsky.social · 28/07/2025

The shift from Type II to Type I function reveals a structure–function continuum for anti-CD20 antibodies, showing that receptor arrangements dictate mechanism of action. RESI provides a platform for structure-guided antibody development, applicable far beyond CD20. (5/6)

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JungmannLab @jungmannlab.bsky.social · 28/07/2025

We showed a direct link between CD20 oligomerization and function by investigating OBZ-based T-cell engagers (TCEs). An increased IgG flexibility in the 2+1 TCE format lead to increased CD20 tetramerization, without higher-order clustering, resulting in a reduction of direct cytotoxicity. (4/6)

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JungmannLab @jungmannlab.bsky.social · 28/07/2025

In contrast, Type II antibodies like Obinutuzumab and H299 induced limited oligomerization to dimers, trimers and tetramers, consistent with their role in promoting direct tumor cell death rather than complement activation. (3/6)

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JungmannLab @jungmannlab.bsky.social · 28/07/2025

By imaging intact cells, we could see these therapeutic antibodies in action: Type I antibodies like Rituximab and Ofatumumab formed extended chains of CD20 hexamers or larger, creating platforms compatible with complement protein binding, mediating cancer cell killing. (2/6)

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JungmannLab @jungmannlab.bsky.social · 28/07/2025

Ever wondered what happens when therapeutic antibodies bind to cancer cells? In our latest study, we used multiplexed 3D-RESI to directly visualize how anti-CD20 antibodies interact with their receptors, revealing their precise arrangement at single-protein resolution. (1/6)

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Max Planck Institute of Biochemistry @mpibiochem.bsky.social · 03/07/2025

Congratulations to Ralf on your election as a new EMBO member: ❕Original press release from @embo.org : www.embo.org/press-releas...

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JungmannLab @jungmannlab.bsky.social · 14/06/2025

Great science, great company and stunning views at our Lab retreat on Schloss Ringberg 🏰🧬🔬. Big thanks to our guests Sabrina Simoncelli, Sebastian Kobold, Thomas Schlichthärle, @massivephotonics.bsky.social & students from the @lfmilles.bsky.social and @mlsb-borgwardt.bsky.social Labs for joining!

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

@moniquehonsa.bsky.social , @philippsteen.bsky.social , Larissa Heinze, Shuhan Xu, Heinrich Grabmayr, Isabelle Pachmayr, Susanne C. M. Reinhardt, Ana Perovic, Jisoo Kwon, Ethan P. Oxley, Ross A. Dickins, Maartje M. C. Bastings, Ian A. Parish

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

Big congrats to @lumasullo.bsky.social and @rafalkowalew.bsky.social who led the project as well as other co-authors that contributed to this work!!

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

To facilitate SPINNA’s widespread use in the scientific community, we offer an open-source Python implementation and a GUI available in the latest version of Picasso (github.com/jungmannlab/..., picassosr.readthedocs.io/en/latest/sp...). 7/7

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

Finally, we investigate the dimerization of CD80 and PD-L1, key surface ligands involved in immune cell signaling. 6/7

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

We further quantitatively evaluate the oligomerization of the Epidermal Growth Factor Receptor (EGFR) upon binding of its ligand, EGF. 5/7

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

We demonstrate SPINNA in DNA-origami, showing that it can infer not only the stoichiometry of the oligomers but also different spatial conformations. 4/7

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

Here, we present SPINNA (Single-Protein Investigation via Nearest Neighbor Analysis): an analysis framework that compares nearest neighbor distances from experimental single-protein data with those from realistic simulations based on a user-defined model of protein oligomerization states. 3/7

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

Latest advances in super-resolution microscopy (DNA-PAINT, MINFLUX, RESI) allow the study of molecular arrangements at the level of single proteins, but extracting quantitative information on the 1–20 nm scale through rigorous image analysis remains a significant challenge. 2/7

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JungmannLab @jungmannlab.bsky.social · 07/05/2025

Understanding how proteins assemble into complexes (oligomerize) within their native cellular environments is crucial for deciphering cellular signaling pathways 1/7

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Monique Honsa @moniquehonsa.bsky.social · 10/04/2025

Big shoutout to co-first authors, Isabelle Pachmayr and Larissa Heinze, for their incredible work and dedication. This work would not have been possible without Levent Bas, @lumasullo.bsky.social, Jisoo Kwon, Ana Perovic, Brenda Schulman, and Ralf Jungmann, as well as the @jungmannlab.bsky.social!

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Eva-Maria Schentarra @evaschentarra.bsky.social · 07/04/2025

One month ago today, I published my first paper with the @jungmannlab.bsky.social 🥳 What better way to celebrate #MicroscopyMonday than with this STAR Protocol on SUM-PAINT spatial proteomic imaging: a guide for highly multiplexed DNA-PAINT imaging in neurons. star-protocols.cell.com/protocols/4066

star-protocols.cell.com

Cell Press: STAR Protocols

STAR Protocols is an open access, peer-reviewed journal from Cell Press. We offer structured, transparent, accessible, and repeatable step-by-step experimental and computational protocols from all are...

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