polyTEM
===================================

**polyTEM** is a Python library for analyzing HRTEM images of polymeric materials. 
polyTEM handles CTF correct, image frame drift correction, backbone chain orientation, 
domain clustering, and statistical analysis of 2D images.


.. note::

   This project is under active development. Documentation is publicly
   available to demonstrate the working applications of this package. 
   Version-controlled source code will be released as manuscripts are published.


References
------------
If you use this package for 2D Analysis, please cite:

.. [ADMA.202409502R1] Cheng, C. et al., Impact of dilute DIO on local microstructure 
   of fluorinated, pNDI-based polymer solar cells. *Advanced Materials*, 2024. https://doi.org/10.1002/adma.202409502

If you use this package for 3D Analysis, please cite:

.. [Dissertation] Cheng, C., "Charge Transport Pathways in Organic Semiconductors: Insights
   From Mesoscale Structural Characterizations." PhD dissertation, Stanford University,
   2024. https://purl.stanford.edu/ts088bt5211


Contributors
-------------
This package was built off of the methods and prototype code
first written and developed by Christopher Takacs, 
Camila Cendra, and Luke Balhorn.

API
----

.. toctree::
   :maxdepth: 2
   
   usage
   api
   3D visualization <3Dviz>