An Integrated Platform, Purpose-Built To Reveal Cellular Choreography
Gather the multi-modal observations necessary to understand the dynamics of living cells, revealing how cells behave and why.
Study What Cells Do, and Why, at Single-cell Resolution, Over Time.
Conventionally, in high-throughput assays, cells are moved between instruments, and in co-culture assays, cell interactions are either averaged in bulk or analyzed at low throughput. This breaks our ability to observe biology in four ways:
- You’re not measuring the same cells. Samples are split, so each assay is run on a different subpopulation.
- If you move the same cells, they suffer. Adherent cells are forced into suspension. Fragile cells die, and those that survive lose continuity, erasing links across modalities, time, and gene expression programs.
- You lose resolution of interactions. Single-cell platforms isolate cells; bulk assays average them. Both miss the heterogeneity of interactions that drive outcomes.
- You end up with fragmented data. Stitching together after the fact, stripping out temporal and multimodal context, weakening signal, making it harder to model mechanism or train reliable models.
Integrated Platform
The Cellanome R3200 platform brings together four core components: instrument, flow cells, assays, and cloud platform.
The R3200 enables measurement of single cells or defined ensembles, keeping individual interacting partners together so coordination and interactions are observed, not inferred. Stimuli, reagents, and readouts are delivered directly to thousands of permeable CellCage™ enclosures, where cells stay in place; viable, trackable, and measurable over time. The platform outputs consistent, multimodal data from the same cells, with the resolution and continuity needed to uncover mechanism, test hypotheses, and train models on intact biological complexity.
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R3200 Instrument: Run Full Experiments Without Moving Your Cells.
The R3200 automates culture, reagent delivery, live-cell imaging, and RNA capture in a single walk-away system. Run longitudinal single-cell or ensemble experiments across tens of thousands of programmable CellCage™ enclosures. Reduce disruption and variation by keeping cells in place, preserving temporal and lineage continuity.
- Programmable cell selection by size, fluorescence, or ensemble composition.
- Brightfield + 4-channel fluorescence (4× and 10× objectives)
- Multi-day experiments with temperature control and programmable media exchange
- Flexible run modes allow for flow cells to be kept on-instrument or moved to an incubator between imaging.
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Fully Automated Workflow With the R3200 Platform
Flow Cell: Track Every Cell’s Story.
Each flow cell contains tens of thousands of programmable CellCage™ enclosures - each a permeable, tunable microenvironment for single cells or defined ensembles.
- Cells remain viable and functional: adherent cells attach, neurons fire, dividing cells proliferate
- Enables co-cultures across a range of effector-to-target ratios
- Longitudinal measurements resolve differential kinetics, capturing both rapid and delayed responses, dynamic trajectories, and transient cell states.
- Uniform conditions across enclosures reduce variability compared to multi-well formats
- Flow cell formats for imaging-only, or RNA-linked experiments
- Surface coatings: Fibronectin, laminin, poly-L-ornithine
Assays & Workflows: Unify Cell Morphology, Behavior, and Underlying Mechanisms.
Cellanome assays and workflows combine a wide variety of cell inputs, treatments, and longitudinal readouts to model biological systems and disease states.
- Perturb with small molecules, antibodies, treatments or CRISPR.
- Combine brightfield and fluorescence imaging, RNA-Seq, CRISPR-Seq, and AI-derived morphotyping from the same cells.
- Apply built-in AI tools to extract morphological fingerprints, revealing subpopulations and state changes that can be missed by RNA-only analysis.
Key features
Cellanome assays and workflows combine a wide variety of cell inputs, treatments, and time-resolved readouts to model biological systems and disease states.
- Fluorescence-based phenotypic and functional assays use standard protocols and commercially available antibodies.
- RNA-Seq and CRISPR-Seq are available via Cellanome kitted reagents.
- AI-based morphotyping is integrated in our standard analysis pipeline, no extra prep or protocols are required.
Build Scalable Models for Disease Research
The Cellanome platform supports a variety of cell types and numerous assays, making it easy to create longitudinal models for studying disease mechanisms and powering drug discovery.
Cellanome Cloud: Where Complexity Becomes Insight.
The Cellanome Cloud platform gets you moving from day one. It's where you design multi-day automated runs and seamlessly explore multimodal results.
- Plan & monitor runs: Configure cell loading, media exchange, imaging routines and perturbation delivery; track progress in real time.
- Integrate datasets automatically: link imaging and sequencing data at the cell or ensemble level.
- Explore and gate: Gate on features of interest and trace subpopulations through longitudinal trajectories, without code.
- Export & analyze: Download raw or structured data (e.g., Seurat-compatible .rds file) supported by rich documentation, analysis vignettes, and Cellanome R packages.
Use the Structure in Your Data to Train Better Models.
Cellanome’s integrated per-cell (or per-ensemble) data object keeps temporal and multimodal measurements linked, so perturbations, phenotypes, interactions, and gene expression profiles can be related within the same experimental context. Consistent experimental conditions across enclosures further reduce noise, making signals easier to detect and compare.
- Time as signal: Use earlier phenotypes to help predict later outcomes, support automated labelling and model asynchronous transitions and dynamic responses.
- Multimodal context: Combine functional and morphological features to disambiguate sparse data and reveal cell states that may not be apparent from RNA alone.
- Model coordinated behaviors: Track ensemble-level dynamics, such as killing or antigen presentation, reveal the programs that underly differential responses.
Integrated, high-dimensional record linking perturbation delivery, morphology, multi-channel fluorescence, and morphological embeddings across time, and end-point RNA/sgRNA readouts.
Support & Services
We’ll help your team get started, and keep moving.
Accelerate your research with proof-of-principle studies, expert support, and tailored service packages.
- Installation and hands-on training
- Expert consultation for transitioning multi-platform workflows onto the Cellanome platform
- Assay development and optimization services
- Ongoing scientific support from experienced researchers