.. contents::

Welcome to Microscope Automation's documentation!
=================================================

.. toctree::
   :maxdepth: 1
   :caption: Overview

   README <self>
   installation
   CONTRIBUTING

.. toctree::
   :maxdepth: 1
   :caption: Orchestrator

   find_positions
   microscope_automation
   write_zen_tiles_experiment

.. toctree::
   :maxdepth: 1
   :caption: Hardware

   hardware_components
   hardware_control
   hardware_control_3i
   hardware_control_zeiss
   RS232
   setup_microscope

.. toctree::
   :maxdepth: 1
   :caption: Samples

   correct_background
   draw_plate
   find_well_center
   find_cells
   interactive_location_picker_pyqtgraph
   positions_list
   samples
   setup_samples
   tile_images

.. toctree::
   :maxdepth: 1
   :caption: Connectors

   connect_slidebook
   connect_zen_blue
   connect_zen_black

.. toctree::
   :maxdepth: 1
   :caption: Settings

   meta_data_file
   preferences
   slidebook_experiment_info
   zen_experiment_info

.. toctree::
   :maxdepth: 1
   :caption: Utility

   automation_exceptions
   automation_messages_form_layout
   error_handling
   get_path
   image_AICS
   load_image_czi
   software_state

.. toctree::
   :maxdepth: 1
   :caption: Import Helpers

   intelligent_imaging_innovations
   zeiss

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

   LICENSE

.. include:: ../README.rst

Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`