ArticleNanophotonics (Berlin, Germany)2025
DeepQR: single-molecule QR codes for optical gene-expression analysis.
Article in Nanophotonics (Berlin, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- A Dispersive Image Scanning Microscope for Multi-color High-resolution Imaging.ACS photonics · 2026Article
- Compact Spectral Encoding Microscopy by Terrace Grating Optics.ACS photonics · 2026Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Optical imaging and single-molecule imaging, in particular, utilize fluorescent tags in order to differentiate observed species by color. The degree of color multiplexing is dependent on the available spectral detection window and the ability to distinguish between fluorophores of different colors within this window. Consequently, most single-molecule imaging techniques rely on two to four colors for multiplexing. DeepQR combines compact spectral imaging with deep learning to enable 4 color acquisition with only 3 spectral detection windows. It allows rapid high-throughput acquisition and decoding of hundreds of unique single-molecule color combinations applied here to tag native RNA targets. We validate our method with clinical samples analyzed with the NanoString gene-expression inflammation panel side by side with the commercially available NanoString nCounter system. We demonstrate high concordance with "gold-standard" filter-based imaging and over a four-fold decrease in acquisition time by applying a single snapshot to record four-color barcodes. The new approach paves the path for extreme single-molecule multiplexing.
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