Sinem Saka

27 Apr

Cells are not just bags of molecules. Function depends on spatial interactions: RNAs and/or proteins come together with interaction partners to drive regulation and function. In our new preprint, we introduce ProPER, a novel method for in situ proximity detection. Preprint: tinyurl.com/muju86s6

Jorge Trojanowski@jorgetrojanowski.bsky.social

1/ ProPER - Our novel ligation-free proximity detection method for efficient multiplexed imaging of molecular interactions in situ. Among other things we use it to image the life cycle of RNA molecules and resolve differential kinetics of gene expression steps. New preprint: doi.org/10.64898/202...

biorxiv.orgUniversal oligo adapters for high-efficiency DNA-barcoded antibody panel generationDNA-barcoded antibodies are central to a broad range of spatial and dissociative assays and applications, including multiplexed imaging, single-cell profiling, and proximity detection. Direct modifica...

If you’ve built DNA-barcoded antibody panels, you know the pain: every barcode means another conjugation. In our new preprint we introduce UnO, which transforms antibody conjugation problem into a universal barcode conversion workflow, enabling rapid panel generation. www.biorxiv.org/content/10.6...

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#4 We validated the approach across both subcellular Immuno-SABER and tissue-based CODEX workflows for multiplexed protein imaging, yielding high-performance panels.

#5 Big thanks to all co-authors -- project leads Valeriy Pak and Yulia Ermakova, and contributors Christina Schniederjohann, Berkan Kanmaz, Robert Reinhardt, Felix Schneider, Tomas Martak, Sascha Dietrich, and Peter-Martin Bruch.

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#2 In our new preprint, we introduce UnO (Universal Oligo Adapter). UnO is a dual-photoreactive adapter that enables rapid covalent and site-directed attachment of user-defined DNA barcodes to small quantities of off-the-shelf antibodies by a simple illumination step in a parallelizable fashion.

#3 Key features: - One universal reagent for site-directed conjugation of any DNA barcode - Rapid generation of custom barcoded panels - Minimal antibody input requirements - Compatibility with off-the-shelf antibodies - Reduced cost, time, and effort during panel development

Many multiplexed detection approaches rely on DNA-barcoded antibodies. But every new barcode typically requires a separate conjugation reaction, making panel development resource-intensive and low-throughput.

20 Mar

Spectral multiplexing is typically limited to 4-5 channels. Our new preprint introduces a framework that utilizes DNA barcoding and signal tuning to enable robust spectral unmixing and ground-truth benchmarking to achieve 15-plex subcellular profiling without cycling www.biorxiv.org/content/10.6...

Kristina@jekristina.bsky.social

Ever felt constrained by the "4-color limit" in fluorescence imaging? We use DNA-barcoded labeling to build high-plex panels, enabling imaging of 15 targets across the full fluorescence spectrum. doi.org/10.64898/202... Grateful to @sinemsaka.bsky.social and all authors for making this possible.

20 Mar

This has been a great collaboration between @embl.org and @leicamicrosystems.bsky.social with contributions from @jekristina.bsky.social @ilastik-team.bsky.social @wvierdag.bsky.social and all co-authors

12 July 2025

I am delighted to co-organize the 2nd #ESSB meeting as an #EMBL Conference, with incredible support of @events.embl.org. Abstract submission deadline is July 15! #ESSB members submitting an abstract are eligible for one of 100 registration subsidy awards (up to 50%). #ESSB2025 #EMBLSpatialBiology

EMBL Events@events.embl.org

‼️ Don't forget to submit your abstract for #EMBLSpatialBiology! The new deadline is 15 July 👉 https://s.embl.org/spb25-01-bl 📅 14–17 Oct 📍EMBL Heidelberg and Virtual ✨ ESSB will provide a fee subsidy for the top accepted abstracts. More info ➡️ https://s.embl.org/SPB25-01-practical-information

embl.orgImaging-based spatial-omics

23 June 2025

We had a lovely week in Heidelberg teaching ins and outs of #spatialbiology, and providing hands-on training for custom protocols like #immuno-saber, #ibex, #hybRISS. Massive thanks to my co-organizers, our dedicated trainers and excellent speakers, and #EMBO, #EMBL & sponsors. #EMBOSpatialOmics

EMBL Events@events.embl.org

🥙 That's a wrap! #EMBOSpatioOmics is officially over. This course provided an introduction to the various methods of spatial-omics. We hope you were able to gain valuable knowledge for your research! 🙌 A big thank you to all of our participants, organisers, speakers, and trainers 👏

31 May 2025

We are happy to participate in the ARISE program and have a range of collaborative opportunities for various backgrounds including biochemistry, imaging, omics or lab automation. Get in touch if interested!

EMBL@embl.org

Interested in research infrastructures career? The #ARISE2 Fellowship Programme might be right for you. MSCA funded, the programme supports STEM researchers in becoming leaders in research infrastructures, driving innovation in life sciences 🧪 🗓️ Call opening: 30 June www.embl.org/training/ari...

3 Mar 2025

We are repeating our EMBO Practical course for imaging-based spatial omics this June in Heidelberg. We will cover sample preparation, multiplexed IF (IBEX and Immuno-SABER), antibody-DNA conjugation, in situ sequencing, data analysis and visualization. Lots of fun and in-depth discussions!

EMBL Events@events.embl.org

Would you like to get a comprehensive introduction to the various methods of spatial-omics and in particular those of multiplex immunofluorescence and spatial transcriptomics? Then apply for #EMBOSpatialOmics by 10 March here 👉 s.embl.org/iso25-01-bl #microscopy #imageanalysis #spatialbiology

1 Jan 2025

The beautiful DNA-microart created by the wonderful Jennifer Heck and Kristina Jevdokimenko in our group to celebrate the festive season: Using Light-Seq, pixels of a DNA canvas was "painted" on a microscope by photocrosslinking DNA barcodes with 3 different fluorophores @embl.org's PhD course '24

13 Dec 2024

The 1st European Society for Spatial Biology (#ESSB) meeting has been a blast! Great talks, exciting posters, new tech platforms and a budding vibrant community - made this a joy beyond our expectations. See you all again next year's edition at @embl.org Heidelberg on 14-17 Oct 2025!