Microscope documentation

Practical guides for opening and annotating whole-slide images, running local workflows, and extending Microscope with Python.

Choose a learning path

• First slide: Open, inspect, and annotate a slide — use the bundled public example or a local WSI, then save or export your work.
• First analysis: Create your first tissue mask — connect the local companion and run WSI Region → Grayscale → Threshold.
• Build with Python: Connect the local companion, then write and run a custom node.
• Author with an agent: Set up MCP workflow authoring, validate a graph, and load it into the viewer for execution.
• Find node schemas: Browse generated node references or begin with the OpenCV guide.

What these guides cover

The viewer guide covers supported single-file formats, navigation, annotations, overlays, projects, settings, and exports. Workflow and Python references explain region transfer, typed graphs, local execution, custom nodes, and MCP's current authoring boundary. Official pack guides describe OpenCV, Double-Pass, Conflux, and InstanSeg; model packs require their documented weights and optional dependencies.

Guides and examples are assembled from explicit allowlists in the six source repositories. The viewer, SDK, and each node-pack repository remain authoritative; the site build does not copy entire documentation directories.