Related Experiment Video
Updated: May 19, 2026
12:52
High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression
Published on: April 18, 2021
Scalable longitudinal imaging and transcriptomics of cells in dynamic enclosures
Tarun K Khurana1, Liz Y Wu1, Pier Federico Gherardini1
1Cellanome Inc., Foster City, CA 94404, USA.
Biorxiv : the Preprint Server for Biology
|May 18, 2026
Summary
This study introduces a new method for tracking cell behavior over time and analyzing their gene activity. This approach reveals adaptive cancer cell states and uncovers key drivers of cellular function.
Area of Science:
- Cell biology
- Genomics
- Biotechnology
Background:
- Cellular dynamics are crucial for understanding health and disease.
- Current single-cell technologies provide only static snapshots, limiting insights into dynamic processes.
- There is a need for methods that link live-cell behavior with molecular profiles.
Purpose of the Study:
- To develop a scalable platform for longitudinal imaging and whole-transcriptome profiling of individual cells.
- To bridge the gap between dynamic cellular phenotypes and their underlying molecular mechanisms.
- To enable deeper characterization of complex cellular states.
Main Methods:
- Integration of light-guided hydrogel polymerization and computer vision for on-demand cell compartmentalization.
- Longitudinal imaging of live-cell behavior within generated compartments.
- Whole-transcriptome profiling of the same cells after imaging.
- Paired analysis of dynamic imaging data and transcriptomic data.
Main Results:
- A novel platform enabling on-demand compartmentalization and paired functional and molecular profiling of live cells at scale.
- Identification of an adaptive, drug-resistant lung cancer cell state associated with potassium channel upregulation and p53-dependent quiescence.
- Discovery of key drivers of adipogenesis and microglial phagocytosis missed by traditional transcriptomic clustering, through joint analysis of imaging and transcriptomic data.
Conclusions:
- Paired functional imaging and transcriptomic analysis is a powerful approach to resolve molecular drivers of complex cellular behaviors.
- The developed platform facilitates a deeper understanding of dynamic cellular processes in both normal physiology and disease.
- This technology opens new avenues for characterizing cellular states and identifying therapeutic targets.
