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4D-Explorer Documentation
==========================

Welcome to the 4D-Explorer documentation. This documentation provides comprehensive guidance on using and contributing to the 4D-Explorer project.

.. image:: /fig/InitWindow.png 
    :alt: 4D-Explorer Main Window

4D-Explorer is a software designed for analyzing four-dimensional scanning transmission electron microscopy (4D-STEM) data. It allows for the import, storage, correction, and reconstruction of 4D-STEM datasets and their metadata in real space. For an overview of 4D-STEM technology, see the review article by `Colin Ophus, 2019`__. 

__ https://www.cambridge.org/core/journals/microscopy-and-microanalysis/article/fourdimensional-scanning-transmission-electron-microscopy-4dstem-from-scanning-nanodiffraction-to-ptychography-and-beyond/A7E922A2C5BFD7FD3F208C537B872B7A

The documentation is organized into several sections:

- **Installation**: Detailed installation instructions for different platforms.
- **Test Dataset**: Description and usage of the provided test datasets for practice and demonstration.
- **Getting Started**: Instructions on how to install and begin using 4D-Explorer.
- **File and Data Operations**: Information on managing and manipulating HDF5 files and datasets.
- **Displaying Data**: Guides on how to visualize 2D images, vector fields, and other data types.
- **Reconstruction**: Methods and techniques for reconstructing images from 4D-STEM data.
- **Calibration**: Detailed steps on calibrating 4D-STEM datasets for accurate and quantitative imaging.

Please navigate through the sections using the table of contents below.

- **Project Repository**: The source code and issue tracker for 4D-Explorer can be found on GitHub at https://github.com/ManifoldsHu/FourDExplorer


.. toctree::
   :maxdepth: 2
   :caption: Table of Contents

   installation
   test_dataset
   getting_started/index
   file_and_data_operations/index
   displaying_data/index
   reconstruction/index
   calibration/index
   license