Functional genomics. Microscopy-native screens.
Biocartesian
Optical pooled screens for cell biology you can see.
With ARADIA™, genomic DNA targets can now be sequenced with a microscope, enabling pooled screens of CRISPR guides, CARs, UTRs, or engineered barcodes for morphological, protein, RNA, spatial, or live-cell phenotypes.
Cell Painting combined with ARADIA™ imaging of CRISPR-Cas9 perturbations
See both together:
Single-cell phenotype
Microscopy-captured live-cell or fixed phenotypes
Single-cell perturbation
Pooled CRISPR guides, CARs, UTRs, or barcodes imaged using ARADIA™
Technology
ARADIA™: Amplified Random Access Detection for In situ Analyses
ARADIA™ is Biocartesian’s proprietary technology for reading targeted DNA sequences in situ, enabling microscopy-captured single-cell phenotypes to be associated with a perturbation from a pooled library.
01
Design pooled library
Design genome-wide or targeted libraries of CRISPR guides, barcodes, CARs, UTRs, or other engineered sequences compatible with ARADIA™.
02
Perturb and culture cells
Deliver a pooled perturbation library to cells. Optionally use separate wells to vary treatments, timepoints, or selection conditions.
03
Image cellular phenotypes
Acquire high-content images and readouts including morphology, Cell Painting, protein, RNA, reporter-based, and live-cell assays.
04
Image perturbations with ARADIA™
Amplify and detect guides, barcodes, or other sequences to link single-cell phenotyping images to a perturbation.
05
Analyze phenotypic images
Analyze perturbation-linked single-cell phenotyping images to uncover targets, pathways, and mechanisms of action.
Why Optical Pooled Screens
Each cell is a data-rich experiment
With ARADIA™ (Amplified Random Access Detection for In situ Analyses), the perturbation delivered to single cells can be sequenced in situ, linking the cell's perturbation to any microscopy-based cellular phenotype. High-content screens can be easily scaled to thousands of perturbations for target discovery, pathway mapping, and mechanism-of-action studies.
What standard screens miss
Pooled NGS / FACS screens
Straightforward for sortable or selectable phenotypes, but unable to capture complex phenotypes
Restricted to selectable or sortable phenotypes
No morphology, localization, cell-cell interactions, or live imaging
Gating decisions lock in one phenotype per experiment
Misses heterogeneous responses
Requires follow-up experiment for rich phenotyping
Arrayed high-content screens
Provide complex phenotypic readouts, but hard to scale to a large number of perturbations
Restricted to fewer perturbations, potentially missing critical hits
Higher automation requirements
Plate effects and batch effects can dominate subtle phenotypes
More expensive per perturbation
Limited room for multiple doses, timepoints, and replicates at scale
Screens using ARADIA™ are designed to combine the scale of pooled screening with the phenotypic richness of microscopy. Start building your database of single-cell phenotypes to serve as a foundational reference of your model system.
Optical pooled screens scoped to meet your team's capabilities
Biocartesian activities
Your team’s activities
01
Design pooled library
02
Perturb and culture cells
03
Image cellular phenotypes
04
Image perturbations with ARADIA™
05
Analyze phenotypic images
Full-service optical screening project
DIY cell culture project
ARADIA™ readout-only project
Reach out to see how you can get started with optical pooled screens.
Book a time
Applications
Microscopy-powered functional genomics
Optical CRISPR screens
Genome-wide or targeted screens with image-based phenotypes using Cas9 knockout, CRISPRi, CRISPRa, Cas13, base-editor-compatible designs, and other barcode-linked perturbation systems.
CAR variant screening
Screen CAR designs, signaling domains, binders, regulatory architectures, or expression cassettes using fixed or live-cell readouts for potency, activation, exhaustion-associated phenotypes, killing dynamics, synapse formation, and target-cell engagement.
UTR and regulatory-element libraries
Screen 5′ UTRs, 3′ UTRs, promoters, enhancers, synthetic regulatory parts, and expression-control elements using reporter expression, RNA abundance, localization, or live-cell dynamics.
Lineage tracing and barcode screens
Use complex barcode libraries to follow clonal behavior, differentiation trajectories, treatment response, spatial organization, or cell-state transitions while preserving microscopy context.
Target discovery and validation
Move from phenotype-rich discovery to focused validation screens that connect candidate genes or perturbations to imaging-based biological outcomes.
Drug response and mechanism-of-action screens
Identify genetic or regulatory drivers of drug response, pathway engagement, resistance, toxicity, localization, morphology, or transcriptional state.
Phenotypic Readout Compatibility
Fixed or live-cell phenotypes
Pooled screening with ARADIA™ is compatible with a wide range of phenotypic readouts.
Fixed-cell readouts
Cell Painting and morphology profiling
Multiplexed immunofluorescence for protein abundance and localization
Spatial transcriptomics for RNA expression and localization
Reporter and pathway-activation markers
Organelle structure and subcellular organization
DNA damage, cell-cycle, apoptosis, and stress phenotypes
Marker colocalization and single-cell heterogeneity
Live-cell readouts
Reporter dynamics and localization
Cell growth and death
Migration and invasion
Differentiation and cell-state transitions
Cell-cell interactions
Immune-cell killing assays
Drug-response kinetics
Don’t see your microscopy-based readout listed? Reach out to discuss whether ARADIA™ can work with your assay.
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WHY BIOCARTESIAN
Collect the foundational dataset for your team’s biology
Biocartesian helps discovery teams connect perturbation identity to image-rich cellular phenotypes with scalable pooled workflows, fast execution, and expert-led project design.
Microscopy-native screening
Designed around visual, spatial, molecular, and live-cell phenotypes from the start.
Pooled scale, fast execution
Move from focused pilots to larger perturbation screens without the cost and logistics of fully arrayed workflows.
Foundational imaging dataset
Generate reusable, cell-level microscopy datasets that can be revisited as new hypotheses, markers, or phenotypic features emerge.
Adaptable to your assay
Work with your cell model, perturbation system, library, marker panel, reporter, treatment, or live-cell workflow.
Full-service or modular
Use Biocartesian for complete screen execution or ARADIA™ readout and analysis.
Expert-led project execution
Attentive scientific project management helps keep screens efficient, well-controlled, and focused on decision-ready outputs.
Not sure where to start?
Contact us today. We can help define the perturbation strategy, imaging readout, and fastest path to a pooled screen.
Full-service screens or modular ARADIA™ support available.
Discuss your project
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