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chore: Enhance documentation (#232)
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‎biome.json‎

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},
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"files": {
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"ignoreUnknown": false,
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"includes": ["**", "!**/dist/**/*", "!**/coverage/**/*", "!**/.astro/**/*"]
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"includes": ["**", "!**/dist/**/*", "!**/coverage/**/*", "!**/.astro/**/*", "!**/*.astro"]
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},
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"formatter": {
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"enabled": true,

‎site/astro.config.mjs‎

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autogenerate: { directory: 'packages' },
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},
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{
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label: 'Developers',
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label: 'Vis Package Developers',
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autogenerate: { directory: 'developers' },
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},
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],

‎site/src/components/PackageManagerTabs.astro‎

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---
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import { Tabs, TabItem, Code } from '@astrojs/starlight/components';
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interface Props {
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npm: string;
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pnpm: string;
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yarn: string;
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}
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const { npm, pnpm, yarn } = Astro.props;
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---
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<Tabs syncKey="pkg">
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<TabItem label="npm">
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<Code code={npm} lang="bash" />
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</TabItem>
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<TabItem label="pnpm">
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<Code code={pnpm} lang="bash" />
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</TabItem>
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<TabItem label="yarn">
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<Code code={yarn} lang="bash" />
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</TabItem>
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</Tabs>

‎site/src/content/docs/getting-started/packages.md‎

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The `AllenInstitute/vis` repository holds multiple published packages. The current list of packages is below:
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- `vis-core`: A collection of useful utilities used to build our big-data, scalable, data visualization tools, including the DZI viewer, OME-Zarr viewer, and our scatterplot tool "Scatterbrain" for the [ABC Atlas](https://knowledge.brain-map.org/abcatlas) in the Brain Knowledge Platform web application
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- `vis-dzi`: A renderer for [Deep Zoom Images](https://en.wikipedia.org/wiki/Deep_Zoom)
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- `vis-geometry`: A collection of vector functions for 2D and 3D geometry
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- `vis-omezarr`: A renderer for [OME-Zarr](https://ngff.openmicroscopy.org/latest/) datasets
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- `vis-core`: A collection of useful utilities used to build our big-data, scalable, data visualization tools, including the DZI viewer, OME-Zarr viewer, and our scatterplot tool "Scatterbrain" for the [ABC Atlas](https://knowledge.brain-map.org/abcatlas) in the Brain Knowledge Platform web application
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- `vis-dzi`: A renderer for [Deep Zoom Images](https://en.wikipedia.org/wiki/Deep_Zoom)
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- `vis-geometry`: A collection of vector functions for 2D and 3D geometry
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- `vis-omezarr`: A renderer for [OME-Zarr](https://ngff.openmicroscopy.org/latest/) datasets
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- `vis-scatterbrain`: A scatterplot viewer optimized for visualizing large datasets, such as those in the [ABC Atlas](https://knowledge.brain-map.org/abcatlas)
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To install and use these packages, see the instructions on [using packages](../using-packages).
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## Future Packages
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- `@alleninstitute/vis-scatterbrain` - Code for building scatterplots
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- `@alleninstitute/vis-react` - React component implementations of each of the visualization packages.
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The following is a list of packages that we would like to create in the future.
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If you are interested in contributing to the development of any of these packages, please reach out on GitHub to get started!
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- `vis-components` - A collection of web components for displaying visualizations built with our `vis` packages
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- `vis-react` - React component implementations of each of the visualization packages
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- `vis-[your favorite framework]` - Any other framework-specific implementations of our visualization packages, as driven by community needs

‎site/src/content/docs/index.mdx‎

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image:
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file: ../../assets/umap.png
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actions:
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- text: Get Started
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link: /vis/getting-started/packages
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variant: primary
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- text: Examples
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link: /vis/examples/omezarr1
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icon: right-arrow
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- text: Read the docs
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link: /vis/getting-started/packages/
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variant: minimal
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variant: secondary
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---
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import { Card, CardGrid } from '@astrojs/starlight/components';
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<CardGrid stagger>
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<Card title="ABC Atlas" icon="rocket">
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The [Allen Brain Cell Atlas (ABC Atlas)](https://knowledge.brain-map.org/abcatlas)
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uses `@alleninstitue/vis-core` to visualize millions of points of data in the browser.
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uses `@alleninstitute/vis-core` to visualize millions of points of data in the browser.
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</Card>
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<Card title="GTA" icon="magnifier">
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The [Genetic Tools Atlas (GTA)](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens/HTS03VQD4BBB67I3BAP)
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uses `@alleninstitute/vis-omezarr` to display OME-Zarr previews.
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</Card>
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<Card title="DZI" icon="information">
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The [SEA-AD project](https://dev-knowledge.brain-map.org/data/JGN327NUXRZSHEV88TN/specimens/JGCXWER774NLNWX2NNR)
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The [SEA-AD project](https://knowledge.brain-map.org/data/JGN327NUXRZSHEV88TN/specimens/JGCXWER774NLNWX2NNR)
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uses `@alleninstitute/vis-dzi` to display Deep Zoom Image (DZI) views.
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</Card>
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</CardGrid>

site/src/content/docs/packages/core.md renamed to site/src/content/docs/packages/core.mdx

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---
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title: Core
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description: Documentation for the `@alleninstiute/vis-core` package
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description: Documentation for the `@alleninstitute/vis-core` package
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---
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import PackageManagerTabs from '../../../components/PackageManagerTabs.astro';
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## Installation
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To install the `@alleninstitute/vis-core` package, make sure you've followed the instructions for [authenticating
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with the Allen Institute's npm registry on GitHub](../../getting-started/using-packages), then run the following command in your terminal:
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<PackageManagerTabs
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npm="npm install @alleninstitute/vis-core"
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pnpm="pnpm add @alleninstitute/vis-core"
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yarn="yarn add @alleninstitute/vis-core"
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/>
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## How To use generic rendering tools for your cool data
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### Use case

‎site/src/content/docs/packages/dzi.mdx‎

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---
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title: DZI
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description: Documentation for the `@alleninstiute/vis-dzi` package
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description: Documentation for the `@alleninstitute/vis-dzi` package
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---
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import { Aside } from '@astrojs/starlight/components';
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import PackageManagerTabs from '../../../components/PackageManagerTabs.astro';
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# Installation
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To install the `@alleninstitute/vis-dzi` package, make sure you've followed the instructions for [authenticating
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with the Allen Institute's npm registry on GitHub](../../getting-started/using-packages), then run the following command in your terminal:
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<PackageManagerTabs
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npm="npm install @alleninstitute/vis-dzi"
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pnpm="pnpm add @alleninstitute/vis-dzi"
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yarn="yarn add @alleninstitute/vis-dzi"
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/>
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## Examples
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There is one DZI example to view:
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- [Linked views with an SVG overlay](../../examples/dzi)
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## Usage
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<Aside type="caution">Docs under construction</Aside>

‎site/src/content/docs/packages/geometry.mdx‎

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---
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title: Geometry
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description: Documentation for the `@alleninstiute/vis-geometry` package
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description: Documentation for the `@alleninstitute/vis-geometry` package
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---
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import { Aside } from '@astrojs/starlight/components';
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import PackageManagerTabs from '../../../components/PackageManagerTabs.astro';
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## Installation
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To install the `@alleninstitute/vis-geometry` package, make sure you've followed the instructions for [authenticating
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with the Allen Institute's npm registry on GitHub](../../getting-started/using-packages), then run the following command in your terminal:
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<PackageManagerTabs
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npm="npm install @alleninstitute/vis-geometry"
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pnpm="pnpm add @alleninstitute/vis-geometry"
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yarn="yarn add @alleninstitute/vis-geometry"
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/>
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## Usage
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<Aside type="caution">Docs under construction</Aside>

‎site/src/content/docs/packages/ome-zarr.mdx‎

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---
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title: OME-Zarr
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description: Documentation for the `@alleninstiute/vis-omezarr` package
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description: Documentation for the `@alleninstitute/vis-omezarr` package
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---
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import { Aside } from '@astrojs/starlight/components';
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import PackageManagerTabs from '../../../components/PackageManagerTabs.astro';
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## Installation
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To install the `@alleninstitute/vis-omezarr` package, make sure you've followed the instructions for [authenticating
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with the Allen Institute's npm registry on GitHub](../../getting-started/using-packages), then run the following command in your terminal:
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<PackageManagerTabs
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npm="npm install @alleninstitute/vis-omezarr"
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pnpm="pnpm add @alleninstitute/vis-omezarr"
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yarn="yarn add @alleninstitute/vis-omezarr"
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/>
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## Examples
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There are three OME-Zarr examples to view:
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- [Basic example with a few selectable datasets that shows the viewer and the dataset metadata](../../examples/omezarr1)
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- [Basic example but using our priority cache from `@alleninstitute/vis-core`](../../examples/omezarr2-priority)
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- [Gallery example of multiple viewers sharing the same web context](../../examples/omezarr3-gallery)
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## Usage
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<Aside type="caution">Docs under construction</Aside>

‎site/src/content/docs/packages/scatterbrain.mdx‎

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---
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title: Scatterbrain
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description: Documentation for the `@alleninstitute/vis-scatterbrain` package
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---
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import { Aside } from '@astrojs/starlight/components';
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import PackageManagerTabs from '../../../components/PackageManagerTabs.astro';
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## Installation
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To install the `@alleninstitute/vis-scatterbrain` package, make sure you've followed the instructions for [authenticating
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with the Allen Institute's npm registry on GitHub](../../getting-started/using-packages), then run the following command in your terminal:
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<PackageManagerTabs
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npm="npm install @alleninstitute/vis-scatterbrain"
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pnpm="pnpm add @alleninstitute/vis-scatterbrain"
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yarn="yarn add @alleninstitute/vis-scatterbrain"
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/>
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## Examples
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There is one Scatterbrain example to view:
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- [Basic example](../../examples/scatterbrain)
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## Usage
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<Aside type="caution">Docs under construction</Aside>

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