.. _navigate-home:

############
**navigate**
############


**navigate** is an open-source Python software for light-sheet microscope control. It
focuses on smart microscopy applications by providing reusable acquisition and
analysis routines, termed :ref:`features <features>`, that can be chained
in arbitrary orders to create custom acquisition protocols.
**navigate** is designed to accommodate the needs of
a diverse user base, from biologists with no programming experience to advanced
technology developers.

**Project Philosophy**
=========================

* Prioritize standard library imports for maximum stability, and minimize external
  dependencies.
* Abstraction layer to drive different camera types, etc.
* Plugin architecture for extensibility.
* Maximize productivity for biological users through robust graphical user
  interface-based workflows.
* Performant and responsive.
* Brutally obvious, well-documented, clean code organized in an industry standard
  Model-View-Controller architecture.

.. note::

   This project is under active development. See our `GitHub repository for updates
   <https://github.com/TheDeanLab/navigate>`_.

.. warning::

    Please be advised that while the Dean Lab has implemented several safeguards in the
    automation of hardware, including but not limited to stage limits, voltage minimums,
    and maximums, are more, there are inherent risks associated with the use of such
    automated systems. Despite these precautions, the complexity and nature of automated
    hardware can lead to unpredictable outcomes. Therefore, the Dean Lab and UT
    Southwestern expressly disclaim any responsibility for any damages, losses, or
    injuries that may arise from or be related to the use of **navigate**.
    Users should be aware of these risks and agree to utilize **navigate** at their own risk.


.. toctree::
   :caption: Getting Started
   :maxdepth: 1

   quick_start
   software_installation
   i_want_to


.. toctree::
   :caption: User Guide
   :maxdepth: 1

   user_guide/hardware/hardware_home
   user_guide/file_formats
   user_guide/gui_walkthrough
   user_guide/setup_microscope
   user_guide/acquiring_home
   user_guide/case_studies/case_studies_home

.. toctree::
   :caption: Development
   :maxdepth: 1

   contributing/software_architecture
   contributing/contributing_guidelines
   contributing/feature_container
   user_guide/restapi
   plugin/plugin_home

.. toctree::
   :caption: Plugins
   :maxdepth: 1

   navigate Plugin Template <https://github.com/TheDeanLab/navigate-plugin-template>
   navigate Confocal Projection <https://github.com/TheDeanLab/navigate-confocal-projection>
   navigate at Scale <https://github.com/TheDeanLab/navigate-at-scale>
   navigate Constant Velocity Acquisition <https://github.com/TheDeanLab/navigate-constant-velocity-acquisition>
   navigate MMCore <https://github.com/TheDeanLab/navigate-mmcore-plugin>
   navigate ilastik Server <https://github.com/TheDeanLab/navigate-ilastik-server>
   navigate Photoactivation <https://github.com/TheDeanLab/navigate-photoactivation>

.. toctree::
   :caption: Reference
   :maxdepth: 1

   implementations/implementations
   api


**Authors**
============
**navigate** includes key contributions from numerous individuals, both past and
present, in `The Dean Lab <https://www.dean-lab.org>`_. Please see the accompanying manuscript
for a full list of contributors. :ref:`Outside contributors  <contributing_guidelines>` are welcome.

**Funding**
============
**navigate** is supported by the

- NIH National Institute of General Medical Science (RM1GM145399).
- NIH National Cancer Institute (1U54CA268072).
- `Simmons Comprehensive Cancer Center <https://www.utsouthwestern.edu/departments/simmons/>`_ Translational Seed Grant.
- `UTSW President's Research Council <https://engage.utsouthwestern.edu/pages/membership-giving/membership-giving---presidents-research-council>`_