.. self-driving multi-scale imaging documentation master file, created by
   sphinx-quickstart on Tue Jul  2 17:26:50 2024.
   You can adapt this file completely to your liking, but it should at least
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Welcome to self-driving multi-scale imaging's documentation!
============================================================

**Self-driving, multi-scale software** is an open-source Python software for custom multi-scale
light-sheet microscope control where the low-resolution guides high-resolution acquisition over hours of imaging.

If you use this code, please cite our preprint:
“Imaging of cellular dynamics in vitro and in situ: from a whole organism to
sub-cellular imaging with self-driving, multi-scale microscopy” by
Stephan Daetwyler, Hanieh Mazloom-Farsibaf, Felix Y. Zhou, Dagan Segal,
Etai Sapoznik, Jill M. Westcott, Rolf A. Brekken, Gaudenz Danuser and
Reto Fiolka: https://www.biorxiv.org/content/10.1101/2024.02.28.582579v1

.. note::

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

.. warning::

    Please be advised that there are inherent risks associated with the use of this software.
    Despite precautions, the complexity and nature of automated software and
    hardware can lead to unpredictable outcomes. Therefore, the Fiolka 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 this software.
    Users should be aware of these risks and agree to utilize this software at their own risk.


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

   software_installation

.. toctree::
   :caption: Code organization
   :maxdepth: 1

   user_interface
   code_structure

.. toctree::
   :caption: Python API references
   :maxdepth: 1

   modules


**Funding**
============
This software is supported by the

- NIH National Cancer Institute (1U54CA268072).
- Swiss National Science Foundation (191347 to S.D)
- NIGMS National Institute of General Medical Sciences (R35 GM133522 to R.F.)

References and API
==================

* :ref:`modindex`