CATMAID

CATMAID, short for Collaborative Annotation Toolkit for Massive Amounts of Image Data, is a web-based platform designed for browsing, annotating, and sharing very large image datasets, with particular emphasis on neuroscience and connectomics. It enables researchers to explore teravoxel-scale electron microscopy and light microscopy volumes, annotate neuronal structures, and construct reconstructions by creating skeletons, marking synapses, and placing landmarks. The system emphasizes collaborative workflows, provenance, and data sharing.

Key features include interactive visualization of image tiles, multi-user annotation with versioning, and a range of annotation tools for tracing neurites, labeling synapses, and annotating cells. Annotations and metadata are stored in a centralized database and can be exported in standard formats such as SWC for neuron morphology. CATMAID provides programmatic access through an API, enabling automation and integration with other tools. It supports permissions, task assignment, and review workflows to facilitate collaborative curation.

Architecturally, CATMAID is a client–server application composed of a web frontend that renders tiled image data and real-time overlays, and a backend that handles data management, authentication, and image tiling. It relies on tile servers to efficiently stream image data and on structured storage for annotations, project metadata, and provenance information.

CATMAID has been adopted by laboratories and consortia worldwide to enable community-based annotation of large imaging datasets. As an open-source platform, it supports customization, extension, and integration with other neuroscience data resources and analysis pipelines.