DeepQR: single-molecule QR codes for optical gene-expression analysis

Jonathan Jeffet, Barak Hadad, Sahar Froim, Kawsar Kaboub, Keren M. Rabinowitz, Jasline Deek, Sapir Margalit, Iris Dotan, Alon Bahabad, Yuval Ebenstein

Research output: Contribution to journalArticlepeer-review

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 fourfold 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.

Original languageEnglish
JournalNanophotonics
DOIs
StateAccepted/In press - 2024

Keywords

  • gene expression
  • machine learning
  • NanoString
  • RNA
  • single-molecule
  • spectral imaging

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Electrical and Electronic Engineering

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