Introduction
Vitessce is a visual integration tool for exploration of spatial single cell experiments. Its modular design is optimized for scalable, linked visualizations that support the spatial and non-spatial representation of tissue-, cell- and molecule-level data. Vitessce integrates the Viv library to visualize highly multiplexed, high-resolution, high-bit depth image data directly from OME-TIFF files and Bio-Formats-compatible Zarr stores.
Architecture#
The diagram below highlights how Vitessce is composed of a top-level <Vitessce/> React component which encapsulates several individual visualization or controller components such as <Scatterplot/> and <Spatial/>.
Configuration#
When using the top-level <Vitessce/> component (or the Python/R widgets), a JSON-based configuration termed the "view config" defines how data is retrieved, which visualization components are rendered, and how different components are coordinated.
To simplify the configuration process, we also provide object-oriented APIs for generating view configs in JavaScript, Python, and R.
Distribution#
Vitessce is distributed in multiple ways, and can be used as a:
- JavaScript package and React component
- Python package and Jupyter widget
- R package and R htmlwidget
Integrations#
Vitessce is being used in the following projects: