Cytely

Cytely is an imaging analysis platform designed to turn biological image data into standardized, reproducible measurements. It targets life science research teams running cell-based assays who need to move from sample to auditable results without building complex analysis pipelines or requiring coding expertise.

The platform is grounded in Data-Driven Microscopy, a peer-reviewed framework for automated, context-specific image acquisition and analysis, published in Cell Reports Methods (2023). Cytely analyzes individual cells and objects at single-cell resolution while retaining spatial and subcellular context.

Getting Started and Workflow

• Analysis is designed to be operational in minutes rather than weeks, with automatic identification of cells and objects requiring minimal parameter tuning.
• Works with existing microscope setups — users scan broadly, upload data, and let Cytely handle analysis without changes to current imaging hardware.
• Supports a smart microscopy loop: users can identify populations of interest through gating and send their coordinates back to the microscope for high-resolution or multi-modal follow-up imaging.
• Once analysis is complete, results are presented as an interactive, explorable dataset rather than raw output requiring further processing.

Core Capabilities

• Spatial single-cell analysis: Cytely analyzes cells and objects at true single-cell resolution, preserving spatial and subcellular context — relevant for studying cell interactions and heterogeneous populations.
• No-code segmentation: Segmentation is powered by pre-trained AI that automatically identifies and profiles cells, debris, and subcellular structures without requiring manual configuration or coding.
• Visual gating: Provides an image flow cytometry-like experience, allowing users to plot any measured morphological or intensity parameter from the initial data-independent acquisition (DIA) scan and gate on populations of interest.
• Sharing and reproducibility: Complete experiments — including raw data, gates, images, and plots — can be shared via a single secure link, enabling collaborators, reviewers, or auditors to access and verify results.

Ready-to-Go Assays

• Phagocytosis Assay: Pre-made analysis workflows automatically identify interacting cells (e.g., phagocytes and prey), count phagocytosis events, and calculate metrics including Multiplicity of Prey (MOP) and Association Percentage. Addresses questions such as uptake rates, prey distribution inside versus outside cells, spatial spread of phagocytosing cells, and morphological differences between high- and low-uptake cells.
• Rapid Cell Count and Classification: Fast quantification of cell populations and contaminants based on morphology.
• Transfection Efficiency Analysis: Identifies transfected cells using intensity thresholds, co-localization, or nuclear versus cytosolic localization criteria.
• Additional workflows: Supports co-culture assays, rare cell detection, and flexible user-defined workflows beyond the pre-validated assay library.

Scientific Validation

• Cytely's methodology is based on a peer-reviewed publication: André et al., "Data-driven microscopy allows for automated context-specific acquisition of high-fidelity image data," Cell Reports Methods, 2023 (doi: 10.1016/j.crmeth.2023.100419; PMC10088093).
• An interactive phagocytosis dataset is available for users to explore gating and analysis outputs before committing to the platform.

Cytely is available as a cloud-accessible platform with a get-started and book-demo entry path. It is positioned for teams that require auditable, shareable results and want to standardize measurement across experiments without building custom analysis infrastructure.