ClearMap Documentation
======================

.. toctree::
    :hidden:
    :maxdepth: 2

    overview
    getting_started
    installation
    usage
    package_organisation
    gui/index
    advanced/advanced_usage
    api
    media
    references

..    static/scripts/cell_map_tutorial
    advanced/wobblystitcher
    cellmap
    tubemap
    scripts/cell_map_tutorial

**Date**: |today| **Version**: |version|

**Useful links**:
`Source Repository <https://github.com/ChristophKirst/ClearMap2>`__ |
`Issues & Ideas <https://github.com/ChristophKirst/ClearMap2/issues>`__ |
`License <../LICENSE>`__

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            <h5>ClearMap</h5>
            <p>High-performance volumetric image analysis</p>
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            <h5>Custom stitching</h5>
            <p>Tile stitching for terabyte-scale datasets</p>
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            <p>Whole-brain cell detection and atlas mapping</p>
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            <h5>Brain vasculature</h5>
            <p>Graph-based vessel network analysis</p>
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            <p>Developmental atlas registration and comparison</p>
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:mod:`ClearMap` is an open source, GPL-licensed program and set of libraries providing high-performance,
easy-to-use tools to analyse TB scale volumetric image datasets using the `Python <https://www.python.org/>`__
programming language.


*ClearMap* has been written for mapping immediate early genes [Renier2016]_
as well as vasculature networks of whole mouse brains [Kirst2020]_


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    .. grid-item-card:: Getting started
        :img-top: static/index_getting_started.svg
        :class-card: intro-card
        :shadow: md

        The getting started guides provide an overview of the *ClearMap* software
        and how to use it. It is recommended to start here if you are new to *ClearMap*.

        +++

        .. button-ref:: getting_started
            :ref-type: ref
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            To the getting started guides

    .. grid-item-card::  GUI
        :img-top: static/gui-symbol.svg
        :class-card: intro-card
        :shadow: md

        The GUI documentation provides an overview of the graphical user interface. If you
        want to perform analysis without writing scripts, this is the place to start.

        +++

        .. button-ref:: gui
            :ref-type: ref
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            To the GUI documentation

    .. grid-item-card::  Advanced usage
        :img-top: static/index_user_guide.svg
        :class-card: intro-card
        :shadow: md

        The user guide provides a detailed description of the *ClearMap* software and how to use it.
        This is meant for more advanced users who want to understand the software in more detail or
        want to write their own scripts.

        +++

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            To the user guide

    .. grid-item-card::  API reference
        :img-top: static/index_api.svg
        :class-card: intro-card
        :shadow: md

        The API reference provides a detailed description of the *ClearMap* modules and functions.
        This will be your go-to place if you want to write your own scripts or understand the
        underlying algorithms.

        +++

        .. button-ref:: api
            :ref-type: ref
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            To the reference guide


Navigating
----------

`Table of Contents <toc.rst>`__ | :ref:`genindex` | :ref:`modindex` | :ref:`search`