Nuanced variations at the molecular, cellular and physiological level among individuals require designing personalized treatments, which are tailored to their unique characteristics. Cellular heterogeneity and the need for personalized therapeutic interventions provide a strong rationale to perform analysis at single-cell level. Emerging technologies, including genome sequencing, proteomics, and imaging protocols are useful techniques to characterize molecular information at single-cell scale. However, some of these techniques such as qRT-PCR and RNA sequencing rely on the extraction of genetic material and do not enable retention of the intracellular spatial resolution of the transcriptome. To preserve spatial information, in situ hybridization methods such as single-molecule fluorescence in situ hybridization (smFISH), which are powerful tools in detecting individual transcripts, have been developed. However, current smFISH methods have certain limitations including, being time-consuming and costly, requiring a high level of expertise, and being constrained to fixed cells and tissues. Hence, the development of automated, affordable single-cell tools for analysis of non-adherent cells is needed to reveal new insights into tumor heterogeneity and therapeutic resistance, elucidate mechanisms of immune response and immunotherapy, and enhance personalized treatment. 

Technology Overview

Researchers at Northeastern developed an on-chip single-molecule fluorescence in situ hybridization microfluidic droplet platform, which performs both in adherent and non-adherent cells. This platform uses a dual-array or multiple-array device capable of generating aqueous microdroplets containing cells within a biocompatible matrix. Moreover, using integrated droplet generation and droplet merging approach in this platform enable simultaneous detection of transcriptome and proteome. Each microdroplet contains one or more cells that are incubated by fluorescent-labeled probes, such as oligonucleotides and antibodies, and then visualized through fluorescent imaging microscopy. This platform is capable of quantitative analysis of gene expression or protein biomarkers in at least 1000 microdroplets (i.e. 1000 groups of two or more interacting cells) within less than 10 hours. Thus, the invention allows assessment of cell activity and the correlation of cell activity with nucleic acid expression and/or protein expression in a rapid manner and at single-cell resolution.
  • Direct and simultaneous assessment of specific proteins and nucleic acid expression in single cells.
  • Rapid detection as compared with standard FISH methodology.
  • Utilization of simple, inexpensive, and portable instrumentation.
  • Provision of the possibility of single-cell analysis in non-adherent cells. 


  • Study of tumor heterogeneity, effects of anti-tumor agents, and therapeutic resistance
  • Clinical diagnoses of diseases demonstrating chromosomal alterations
  • Elucidation of immune response mechanisms and designing immunotherapy


  • Technology available for exclusive and non-exclusive licensing
  • Development partner
  • Commercial partner
Patent Information:
For Information, Contact:
Vaibhav Saini
Senior Manager Commercialization
Northeastern University
Tania Konry
Saheli Sarkar