COSC 499 Project 2 NRC Electron Microscope Tools

A set of Python tools re-written from Matlab for use with electron microscopes.

Alignment Software: Tomography image sequence alignment, tracking and optimization

video demo w/ voice over: https://www.youtube.com/watch?v=eJnH7GQfo_c

NanoMi Optics: Optics diagram and optimization for Nanomi transmission electron microscope

qEELS: Momentum-resolved electron energy loss spectroscopy peak detection

Documentation

• Scope & Charter
• Design
• Communication
• Weekly Logs
• Final

Team Members

• Garrett Cook
• Jasmine Mishra
• Jose Pena Revelo
• Lucas Towers

Intro

Each software is its own python project. The following steps can be applied to all projects.

Windows Users Installation and Usage

1. Install a stable version of Python 3 (must be >=3.9)
2. Extract the full source code to a folder on your device.
3. Run the install.py in a given project with python.
4. Run the main.py in a given project with python.

Mac/Linux Installation and Usage

1. Install a stable version of Python 3 (must be >=3.9), using a package manager such as brew or apt is recommended.
   • brew install python@3.9
   • sudo apt install python3.9
2. Install supporting libraries for Tcl/Tk
   • brew install python-tk
   • sudo apt install python3-tk
3. Extract the full source code to a directory on your device.
4. Run the project's install.py with python.
5. Run the project's main.py with python.

Run via command line

python -m qeels
python -m nanomi_optics
python -m alignment_software

Advanced Development Instructions

1. Install Poetry for Python
2. Clone the repository and cd into one of three projects directories
3. Install dependencies with poetry install
4. Enter a virtual shell with poetry shell
5. Run tests with pytest
6. Lint code with flake8 <package_name>