TEMWizard is used to visualize intermediate and final results from Atomap, an open-source software tool for determining the position and other features of atomic columns in transmission electron microscopy (TEM) images. TEMWizard provides an easy-to-use graphical user interface (GUI) for Atomap, allowing the user to provide correct inputs and visualize lattice displacements for analysis of phenomena such as octahedral rotations or bond distortions. It is built atop Python and D3, using the Atomap library integrated in Flask, a Python web framework.

To learn more about Atomap see the following:

• Nord, M., Vullum, P. E., MacLaren, I., Tybell, T., & Holmestad, R. (2017). Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting. Advanced Structural and chemical imaging, 3(1), 1-12.

• Visit the Atomap webppage https://atomap.org/

This code was developed under support by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award #10122.

1. Update filename and click "Rerun Atomap on current page" to reload

1. Download or clone the repository

2. Open Terminal

3. cd to the folder "flask" within temwizard (example below, you can type cd in Terminal and then drag the flask folder to the terminal to quickly get the address)

cd flask

4. create virtual environment

conda create -n temwizard_env python=3.7

5. activate virtual environment

conda activate temwizard_env

6. Install all necessary packages

pip install -r requirements.txt

7. run flask

flask run

8. Go to local address

http://127.0.0.1:5000

9. Follow directions under "How to use TemWizard"

If you find this application useful and want to publish your results, please cite our publication:

Wang, L., Zhao, J., Kuo, C-T., Matthews, B.E., Oostrom, M.T., Spurgeon, S.R., Bowden, M.E., Lee, S-J., Lee, J-S., Guo, E-J., Wang, J., Chambers, S.A., and Y. Du. “Synthesis and electronic properties of epitaxial SrNiO3/SrTiO3 superlattices.” Physical Review Materials. (2022). https://doi.org/10.1103/PhysRevMaterials.6.075006

For questions about TEMWizard usage, contact Marjolein Oostrom ([email protected]) or Steven Spurgeon ([email protected]).

This work is supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award #10122 at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for the U.S. Department of Energy (DOE) by Battelle Memorial Institute under Contract No. DE-AC05-76RL0-1830.

This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.

Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

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TEMWizard Copyright © 2022, Battelle Memorial Institute

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