118 lines
4.9 KiB
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118 lines
4.9 KiB
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.. _navigate-home:
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############
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**navigate**
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############
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.. image:: https://img.shields.io/badge/Published%20in-Nature%20Methods-blue
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:target: https://doi.org/10.1038/s41592-024-02413-4
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:alt: Published in Nature Methods
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.. image:: https://img.shields.io/github/stars/TheDeanLab/navigate?style=social
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:target: https://github.com/TheDeanLab/navigate
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:alt: GitHub Stars
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.. image:: https://img.shields.io/pypi/v/navigate-micro
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:target: https://pypi.org/project/navigate-micro/
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:alt: PyPI Version
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.. image:: https://img.shields.io/pypi/pyversions/navigate-micro
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:target: https://pypi.org/project/navigate-micro/
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:alt: Python Versions
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**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 together arbitrarily to create custom acquisition protocols. **navigate** is accompanied by `Altair <https://thedeanlab.github.io/altair/>`_, our open-source light-sheet microscope designs. **navigate** is designed to accommodate the needs of a diverse user base, from biologists with no programming experience to advanced technology developers.
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**Key Features**
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================
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- Smart microscopy control with customizable acquisition protocols
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- Hardware abstraction layer supporting multiple device vendors
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- Intuitive GUI for biologists with no programming experience
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- Extensible plugin architecture for developers
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- Integration with open-source light-sheet microscope designs
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.. seealso::
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This project is under active development. See our `GitHub repository for updates <https://github.com/TheDeanLab/navigate>`_.
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.. warning::
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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.
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.. toctree::
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:caption: Getting Started
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:maxdepth: 1
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01_getting_started/01_quick_start/01_quick_start
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01_getting_started/02_software_installation/02_software_installation
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01_getting_started/03_i_want_to/03_i_want_to
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.. toctree::
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:caption: User Guide
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:maxdepth: 1
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02_user_guide/01_supported_hardware/hardware_home
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02_user_guide/02_file_formats/file_formats
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02_user_guide/03_user_interface_walkthrough/user_interface_walkthrough
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02_user_guide/04_microscope_setup/setup_microscope
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02_user_guide/05_acquiring_data/acquiring_home
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02_user_guide/06_case_studies/case_studies_home
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.. toctree::
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:caption: Development
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:maxdepth: 1
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03_contributing/01_contributing_guidelines/01_contributing_guidelines
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03_contributing/02_developer_install/02_developer_install
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03_contributing/03_software_architecture/software_architecture
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03_contributing/04_feature_container/feature_container
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03_contributing/05_restapi/restapi
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03_contributing/06_plugin/plugin_home
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.. toctree::
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:caption: Troubleshooting & Known Issues
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:maxdepth: 1
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04_faq/troubleshooting/troubleshooting_home
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04_faq/issues/issues_home
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.. toctree::
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:caption: Plugins
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:maxdepth: 1
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navigate Plugin Template <https://github.com/TheDeanLab/navigate-plugin-template>
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navigate Confocal Projection <https://github.com/TheDeanLab/navigate-confocal-projection>
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navigate at Scale <https://github.com/TheDeanLab/navigate-at-scale>
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navigate Constant Velocity Acquisition <https://github.com/TheDeanLab/navigate-constant-velocity-acquisition>
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navigate MMCore <https://github.com/TheDeanLab/navigate-mmcore-plugin>
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navigate ilastik Server <https://github.com/TheDeanLab/navigate-ilastik-server>
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navigate Photoactivation <https://github.com/TheDeanLab/navigate-photoactivation>
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.. toctree::
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:caption: Reference
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:maxdepth: 1
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05_reference/implementations/implementations
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05_reference/api
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**Authors**
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============
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**navigate** includes key contributions from individuals both inside and outside of `The Dean Lab <https://www.dean-lab.org>`_. Please see the GtiHub repository for a full list of contributors. We welcome community contributions - see our :ref:`contributing guidelines <contributing_guidelines>` for more information on how to get involved.
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**Funding**
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============
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- Cancer Prevention and Research Institute of Texas (10068451).
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- NIH National Institute of General Medical Science (RM1GM145399).
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- NIH National Cancer Institute (1U54CA268072).
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- Simmons Comprehensive Cancer Center Translational Seed Grant.
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- UTSW President's Research Council
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