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Lab"},"license":"MIT","homepage":"https://github.com/bitroc-ai/annota#readme","keywords":["pathology","annotation","openseadragon","whole-slide-imaging","digital-pathology","react","cell-counting"],"repository":{"type":"git","url":"git+https://github.com/bitroc-ai/annota.git"},"description":"An annotation framework for React and Svelte","maintainers":[{"name":"hughlv","email":"hugh.lv@gmail.com"}],"readme":"<p align=\"center\">\n  <img src=\"https://github.com/bitroc-ai/annota/blob/main/docs/public/logo.svg\" alt=\"Annota Logo\" width=\"100\" />\n</p>\n\n# Annota\n\nAnnota is a framework-independent annotation engine for large, zoomable images. Digital pathology\nis its primary use case, but the core model deliberately understands only annotations, geometry,\nlayers, spatial candidates, interaction, history, and rendering. Cell, nucleus, diagnosis,\nrelationships, statistics, and persistence belong to the application domain.\n\n## Installation\n\n```bash\nnpm install annota openseadragon\n# Install only the framework integration you use:\nnpm install react react-dom\n# or\nnpm install svelte\n```\n\nReact and Svelte are optional peers. Canonical imports are separated:\n\n```ts\nimport { createAnnotator, type AnnotationInput } from 'annota';\nimport { AnnotaProvider, Viewer, Annotator, useAnnotator } from 'annota/react';\nimport { AnnotaProvider, Viewer, Annotator } from 'annota/svelte';\nimport { PointTool, PolygonTool } from 'annota/tools';\nimport { loadH5Masks, loadInstanceMask } from 'annota/loaders';\nimport 'annota/styles.css';\n```\n\nThe root package is framework-independent. Existing React consumers can temporarily migrate root\ncomponent imports through `annota/legacy-react`; that compatibility entry and\n`annota/dist/index.css` are deprecated since 0.11 and planned for removal in 2.0.\n\n## Framework-independent usage\n\n```ts\nconst annotator = await createAnnotator({\n  viewer,\n  annotations: [{\n    id: 'region-1',\n    layerId: 'regions',\n    shape: {\n      type: 'polygon',\n      points: [{ x: 10, y: 10 }, { x: 80, y: 10 }, { x: 40, y: 60 }],\n    },\n    properties: { reviewState: 'pending' },\n  }],\n});\n\nconst dispose = annotator.events.on('annotation:update', event => {\n  if (!event.context.transient) persist(event.annotation);\n});\n\ntry {\n  annotator.annotations.update('region-1', {\n    properties: { reviewState: 'approved' },\n  });\n} finally {\n  dispose();\n  annotator.destroy();\n}\n```\n\nAnnota computes and freezes geometry bounds on every write. Public collections are detached\nsnapshots; all stable writes pass through the façade, history, transaction, event, store, spatial,\nand rendering pipeline. Geometry operations reject results containing holes with\n`GEOMETRY_UNSUPPORTED` because the current shape model cannot represent interior rings; they never\nsilently fill those holes.\n\n## Capability API\n\n- `annotations`: add, batch upsert, patch, remove, replace, get, and list.\n- `selection`: set, clear, and read selected IDs.\n- `layers`: create, update, remove, and control visibility, opacity, lock, and z-index.\n- `spatial.search`: fast bounds candidates only.\n- `geometry`: exact intersects, contains, intersection, IoU, merge, and split operations.\n- `history`: undo, redo, state, and clear.\n- `events`: typed, disposable subscriptions with `source`, `transactionId`, and `transient`.\n- `tools`: active interactive tool boundary.\n\nLayer z-index controls only drawing order. Hidden layers are excluded from rendering and hit\ntesting; locked layers remain readable and visible but cannot be edited by users or tools.\n\n## Domain mapping for instance masks\n\nThe core decoder does not interpret class IDs:\n\n```ts\nconst annotations = await loadInstanceMask(buffer, {\n  decodePixel(pixel) {\n    const instanceId = (pixel.r << 8) | pixel.g;\n    return instanceId === 0\n      ? null\n      : { instanceId, attributes: { classId: pixel.b } };\n  },\n  mapProperties(instance) {\n    return {\n      entityType: 'cell',\n      cellClass: mapClass(instance.attributes?.classId),\n    };\n  },\n});\n```\n\nWithout `mapProperties`, output contains only generic source, instance ID, attributes, and area.\n\n## Performance\n\nAnnota uses PixiJS, viewport culling, R-tree candidate queries, cached rendering, and fixed-seed\nbenchmarks. Run `pnpm build && pnpm benchmark` for the reproducible 1k/10k/50k core workload.\nHardware-dependent frame-rate claims are intentionally not published without a fixed browser and\ndevice result.\n\n## Development and migration\n\n```bash\npnpm install\npnpm typecheck\npnpm exec vitest run\npnpm build\npnpm --dir docs build\npnpm test:consumer\npnpm benchmark:ci\n```\n\nSee [the migration guide](docs/src/content/docs/guides/migration-1-0.mdx),\n[CONTRIBUTING.md](CONTRIBUTING.md), and [PUBLISHING.md](PUBLISHING.md).\n\n## License\n\nMIT\n","readmeFilename":"README.md"}