CellCage™ Technology Brings Wells to Cells
By keeping cells in place, the R3200 creates an open canvas for experimental design, enabling characterization of diverse cell types and combinations with linked read-outs.
Time and Context Matter in Cell Biology
In biology, what you see depends on when and how you look. Function emergeover time, through dynamic interactions.A single cell can run multiple functional programs at once. RNA profiles hint at pathways, but post-transcriptional control and context determine whether they become action. Even under the same stimulus, responses vary in timing, type, and duration, often unfolding over hours to days.
Why current workflows miss the full picture
- Transient changes disappear: Without longitudinal, single-cell or single-ensemble data, early-, late-, or non-responders are averaged together and obscured.
- Connections are broken: Measuring each readout separately in different cells severs the link between inputs and outcomes, leaving only correlation and guesswork.
- Biology is distorted: Stripping cells from neighbors or forcing adherent cells into suspension can alter behavior and reduce viability.
Cellanome CellCage™ Technology
CellCage™ technology keeps biology intact
Follow the same cells or ensembles over time, capture movement, interactions, and functional changes - what we call cellular choreography - and link these observations directly to transcriptomic profiles and sgRNA expression from the same cells.
Understand the core workflow
The R3200 platform combines fluorescent imaging, AI-powered cell segmentation, and micro-3D printing to build customized CellCage enclosures – isolating live cells for extended culture, functional assays and transcriptomic profiling, all in one run.
Cellanome’s Core Innovations
Cellanome’s platform brings together a set of proprietary innovations to reveal cellular behavior, interactions, and molecular programs in ways that static snapshots and fragmented approaches cannot.
Programmable Enclosures
Isolate single cells or defined ensembles with media exchange.
- 3D printed microstructures, tunable in shape, size, and permeability, isolate single cells or defined ensembles. Thousands of CellCage Enclosures (CCEs) fit in each flow cell lane. Media and reagent exchange support extended culture and precise delivery of macromolecules. Certain configurations permit signaling across the enclosure wall, enabling, for example, the study of individual neuron somas within a live network, or improved viability for cell types that depend on cues from neighbors.
Photopatterned Cell Isolation
Use real-time imaging and AI to isolate cells of interest in minutes.
- Real-time brightfield and fluorescent imaging, combined with AI-driven algorithms, identify target cells. A digital micromirror device polymerizes enclosures around them in seconds, based on criteria like morphology, marker expression, or co-localization. Tens of thousands of CCEs can be formed in under 15 minutes.
Surface Customization & Coordinate Linking:
Functionalized flow cell surface supports cell adhesion and data traceability.
- The flow cell surface serves many purposes: it forms the floor and ceiling of each CCE, supports adherent cell attachment via customizable coatings and links CCE location to RNA-seq and/or CRISPR-seq data. Embedded fiducials enable coordinate-based alignment, allowing third-party imaging to map back to individual CCEs and integrate into the unified data object.
Lane-based Architecture and Laminar Flow:
Controlled flow for washout, pulsing, and sequential dosing.
- Each flow cell lane is physically isolated, allowing condition-specific experiments to run in parallel. Unlike plate-based systems, where residual compounds or diffusion make true washout difficult, the Cellanome platform enables baseline measurement, compound pulsing, and sequential treatments.
Unified Data Architecture:
Link live cell behavior to transcriptomic signatures.
- Every CCE acts as a matched input-output unit, with a unique identifier linking live-cell observations over time to end-point RNA readouts. All measurements are structured into a unified object within our cloud analysis suite, enabling precise alignment across timepoints and modalities.
Connect Genotype to Function with Linked Data
Cellanome’s platform captures behavior, morphology, and gene expression from the same cells, across time and alongside their interacting partners.
Universal Toolkit for Cell Biology
Gain Deeper Insights For Discovery and Modeling of Complex Biology
As biology embraces AI-guided discovery, CRISPR-based perturbations, in silico modeling, and lab-in-the-loop experimentation, its frontier is increasingly shaped by data and computation. Cellanome delivers rich, connected data built for this era, grounding predictive models in real biological trajectories and opening new possibilities for mechanistic understanding and more effective interventions.
- Track Dynamics With Precision: Follow resistance pathways, functional shifts, and cell-cell interactions over days to weeks, without disrupting native morphology. Simulate chronic, acute, and sequential treatment regimens in disease-relevant contexts.
- Build High-Quality Training Data at Scale: Generate structured, time-resolved datasets under consistent conditions and defined perturbations to reduce imputation, resolve complex states, and train robust, interpretable models.
- Advance Broad Applications: Unlock insights in immunology, oncology, neurobiology, and aging fields where dynamic interactions, multi-modal readouts, and support for adherent cells are essential.
Trusted by Leading Researchers
Researchers across academia and industry are using Cellanome to investigate neuronal networks, immune interactions, and perturbation-response studies (among other applications), uncovering novel insights that are shared at leading scientific conferences.
In this poster presentation, James Walker, PhD, of the Salk Institute, shares data on how the Cellanome platform is enabling single-cell analysis of individual plant cells, such as those from Arabidopsis and Marchantia. James shares how:
• The Cellanome platform enables simultaneous collection of phenotypic and transcriptomic data from thousands of individual plant cells.
• This technology bridges the gap between real-time imaging and single-cell sequencing, advancing the study of plant biology at unprecedented scale and detail.
In this poster presentation, Nick Elder, PhD, highlights how the Cellanome platform empowers neuroscience research by enabling the precise study of brain cell networks, interactions, and individual neuronal behavior. Nick shares how:
• The Cellanome Platform enables comprehensive and long-term analysis of neural networks and individual cell behaviors within controlled, tissue-like environments.
• The technology integrates advanced imaging, tissue culture, and single-cell transcriptomics for next-level studies of brain function and disease.
In this poster presentation, Jiwoon Park, PhD, of Weill Cornell Medicine, demonstrates how the Cellanome platform is advancing CAR T cell therapy research by enabling detailed, scalable assessments of immunotherapy potency and behavior. Jiwoon shares how:
• The Cellanome platform enables scalable, quantitative CAR T cell screening with real-time monitoring of cancer cell killing.
• The system allows for precise control of experimental conditions and integrates multimodal data (imaging and genomics) to enable quantification of variability in CAR T responses in tumor cells.
In this poster presentation, Teresa Ai, PhD, shares how the Cellanome platform can transform drug discovery and development by enabling high-resolution, single-cell analysis to uncover hidden mechanisms of drug response. Teresa shares how:
• The Cellanome platform integrates functional assays and real-time imaging with transcriptomics to track cell fate and pathways.
• This technology is poised to enable dynamic, single-cell tracking and novel disease modeling, supporting design and optimization of next-generation therapies across a wide range of biomedical research areas.
Let’s Talk About Your Experiments
Tell us a bit about your work, and we’ll connect you with a Cellanome scientist with experience on similar studies.