# BisQue Docs

> Guides for exploring, annotating, and analyzing scientific data with BisQue.

Each link is the Markdown source of a documentation page.

## Get started

- [Quickstart](/docs/getting-started/quickstart.md): Upload scientific data, inspect it, and organize it in a BisQue project.

## Concepts

- [How BisQue organizes your work](/docs/concepts/how-bisque-works.md): Understand the objects that connect data, annotation, and analysis in BisQue.
- [Modules and workflows](/docs/concepts/modules-and-workflows.md): Understand analysis modules, workflow revisions, runs, and artifacts.
- [Projects, annotations, and branches](/docs/concepts/projects-and-annotations.md): Learn how projects coordinate collaborators, labels, resources, and annotation history.
- [Resources and datasets](/docs/concepts/resources-and-datasets.md): Learn how BisQue stores data, metadata, collections, and access rules.

## Guides

- [Build and run a workflow](/docs/guides/build-run-workflow.md): Build a repeatable analysis graph and run it against project data.
- [Create an annotation project](/docs/guides/create-annotation-project.md): Create a project, add resources, and begin an annotation task.
- [Upload scientific data](/docs/guides/upload-data.md): Upload files, scientific images, and archives through the BisQue web interface.

## Developer reference

- [API overview](/docs/developer/api-overview.md): Discover BisQue's HTTP API, interactive reference, and contract conventions.
- [Authentication](/docs/developer/authentication.md): Authenticate browser, CLI, notebook, and service clients to BisQue.

## Self-hosting

- [Run BisQue locally](/docs/operations/local-development.md): Start the supported BisQue development environment and find its local services.

## Contribute

- [Documentation roadmap](/docs/contributing/documentation-roadmap.md): Planned work for turning this foundation into complete product documentation.