```{include} ../README.md
```


```{toctree}
:caption: Getting started
:name: getting_started
:hidden:
:maxdepth: 1

getting_started/installation
getting_started/conda
getting_started/apptainer
getting_started/docker
getting_started/pixi
```



```{toctree}
:caption: Usage Notes
:name: usage
:hidden:
:maxdepth: 1


usage/cli
usage/quick
usage/tutorial_inputs
usage/specializedScans
usage/templates
usage/faq
```


```{toctree}
:caption: Processing pipeline details
:name: pipeline_details
:hidden:
:maxdepth: 2

pipeline/pipeline
pipeline/algorithms
```



```{toctree}
:caption: Outputs of HippUnfold
:name: outputs
:hidden:
:maxdepth: 2

outputs/output_files
outputs/visualization
outputs/QC
```



```{toctree}
:caption: References
:name: contributing
:hidden:
:maxdepth: 2

contributing/references
```