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Novel CellCage™ technology integrates image-based phenotyping and single-cell transcriptomics to study dynamic behaviors of living cells

December 1, 2025

ASCB | American Society of Cell Biology

Frank Charbonier, Ph.D., Biomaterials Scientist

Keywords: Image-based phenotyping, Single-cell transcriptomics, Multi-modal analysis, Live-cell dynamics, R3200 Platform, CellCage™ technology

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Leveraging the R3200 Platform and its foundational CellCage™ technology, this research demonstrates the integration of biocompatible, light-guided hydrogel microenvironments to bridge the gap between live-cell imaging and high-resolution transcriptomics. By securing individual cells or defined groups in configurable enclosures, the platform enables the long-term study of phagocytosis, cell-cell interactions, and calcium signaling. This integrated approach allows for the direct mapping of complex, image-based phenotypes to underlying genetic programs, providing a scalable alternative to traditional droplet or nanowell methods

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Case Study: Functional Profiling of Microglia in Neuroinflammation

Link microglial behavior to gene expression at single-cell resolution, for insight into neuroinflammation, drug response, and immune dysfunction in CNS disease.

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Phagocytosis assay in CellCage enclosures - (click to expand image).

Researchers used the Cellanome R3200 to enclose individual microglia with fluorescent particles and track phagocytosis over 12 hours via fluorescent imaging. Each cell’s transcriptome was then sequenced, linking activity levels to gene expression.

What they found:

High-activity microglia upregulated genes in complement signaling, lipid metabolism, and lysosomal function–key pathways in neuroinflammation and repair.

Why it matters:

This approach overcomes key limitations in standard assays by capturing phagocytic function and gene expression in the same individual cells without dissociation, pooling, or inference. It enables a direct, scalable readout of immune heterogeneity, and reveals the transcriptional programs driving effective or impaired microglial responses.

‍What’s next:

Extend to co-cultures by layering enclosed microglia over intact neuronal networks. Study how cell-cell interactions shape phagocytic behavior and fate. Combine with cytokines, CRISPR libraries, or immunotherapies to generate time-resolved, multi-modal datasets that can be used for MoA analysis, early biomarker discovery, and AI-guided modeling in CNS disease.

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Case Study: Modeling Synapse Formation and Developmental Trajectories in 3D

Track development, function, and gene expression in intact neurospheres, a human-relevant 3D model increasingly vital as regulators move away from animal studies.

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Neurospheres in windowed cages that allow them to reach out to form a synapse - (click to expand image).

Stem-cell-derived neurospheres offer a robust 3D model of early brain development, but standard assays disrupt their structure and miss critical dynamics.

Approach:

Using the Cellanome R3200, the research team explored,

Hundreds of intact neurospheres (100–200 cells each) were cultured inside individual CellCage™ enclosures.
Axon extension, synapse formation and calcium activity were tracked over multiple days.
End-point RNA-Seq was linked back to each neurosphere’s functional behavior.
UMAP clustering revealed lineage-specific gene programs, validated by fluorescent markers.

‍What's next:

This lays the groundwork for CRISPR-based multimodal screens to probe mechanisms of development, degeneration, and repair within preserved 3D architecture.

‍Why it matters:

As the FDA and others move to reduce reliance on animal models, human-relevant in vitro systems like this are increasingly essential.

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FAQ's

How does CellCage™ technology on the R3200 Platform differ from standard nanowell or droplet-based methods?

Unlike static well-plates or droplets, CellCage™ enclosures (CCEs) are biocompatible hydrogel microenvironments that can be configured in size, shape, and porosity. This allows the R3200 Platform to support the longitudinal culture of suspension or adherent cells for weeks while maintaining permeable walls for nutrient exchange and real-time monitoring.

How is the R3200 Platform used to link dynamic behaviors to transcriptomic data?

The R3200 Platform facilitates continuous, high-resolution imaging of dynamic behaviors—such as microglial phagocytosis or T-cell activation—while cells are secured within CCEs. Following the observation period, the platform performs direct transcriptomic profiling on those same individual cells, providing a definitive link between a cell's observed history and its molecular state.

What emerging capabilities does the R3200 Platform enable through selective degradation?

Utilizing the R3200's ability to selectively degrade CellCage™ enclosures with cell-compatible chemistry, the technology enables the enrichment or retention of specific target cells from mixed populations. This allows for focused functional profiling and transcriptomic analysis of rare subsets, such as NK cells from unlabeled PBMC mixes, within a single integrated workflow.

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