MagScope Documentation
======================

|pypi| |docs| |doi| |git|

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   :target: https://pypi.org/project/magscope/
   :alt: PyPI

.. |docs| image:: https://img.shields.io/readthedocs/magscope/latest.svg
   :target: https://magscope.readthedocs.io
   :alt: Docs

.. |doi| image:: https://img.shields.io/badge/DOI-10.1101/2025.10.31.685671-blue
   :target: https://doi.org/10.1101/2025.10.31.685671
   :alt: DOI

.. |git| image:: https://img.shields.io/badge/GitHub-MagScope-181717?logo=github&logoColor=white
   :target: https://github.com/7jameslondon/MagScope
   :alt: GitHub

MagScope is a Python framework for live data acquisition and analysis in magnetic tweezers microscopy.

.. grid:: 2
   :gutter: 2

   .. grid-item-card:: Getting Started
      :link: getting_started
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`rocket;3rem;sd-text-secondary`

      How to install and get the demo running

   .. grid-item-card:: User Guide
      :link: user_guide
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`book;3rem;sd-text-info`

      How to use MagScope

   .. grid-item-card:: (Optional) GPU Acceleration
      :link: gpu_guide
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`cpu;3rem;sd-text-success`

      How to use a NVIDIA GPU to speed up image processing

   .. grid-item-card:: Connect Your Camera
      :link: connect_camera
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`device-camera-video;3rem;sd-text-success`

      How to get your lab's camera connected to MagScope

   .. grid-item-card:: Connect Your Hardware
      :link: connect_hardware
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`gear;3rem;sd-text-success`

      How to get your lab's hardware (motors, stage, lights, ect) connected to MagScope

   .. grid-item-card:: Scripting
      :link: scripting_guide
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`terminal;3rem;sd-text-success`

      Automate tasks with Python scripts

   .. grid-item-card:: GitHub
      :link: https://github.com/7jameslondon/MagScope
      :link-type: url
      :text-align: center
      :shadow: md

      :octicon:`mark-github;3rem;sd-text-dark`

      Source code, issues, and releases.

   .. grid-item-card:: Changelog
      :link: https://github.com/7jameslondon/MagScope/blob/master/CHANGELOG.md
      :link-type: url
      :text-align: center
      :shadow: md

      :octicon:`history;3rem;sd-text-info`

      Release-oriented summaries of notable changes.

   .. grid-item-card:: (Advanced) API Reference
      :link: api/index
      :link-type: doc
      :text-align: center
      :shadow: md

      :octicon:`code;3rem;sd-text-dark`

      Full module documentation.

Support
-------

| You can report issues and make requests on the `GitHub issue tracker <https://github.com/7jameslondon/MagScope/issues>`_.
| Having trouble? Need help? Have suggestions? Want to contribute?
| Email us at magtrackandmagscope@gmail.com


.. toctree::
   :hidden:

   getting_started
   user_guide
   gpu_guide
   connect_camera
   connect_hardware
   scripting_guide
   scripting_commands