NUANCE Tech Talk 2024 - Electron Microscopy Data Analysis Crash Course

Python codes for EM analysis presented at NUANCE Tech Talk on May 16, 2024

Introduction

This crash course provides a series of Jupyter notebooks designed to introduce techniques for analyzing electron microscopy data using Python. The course covers various dataset dimensions from simple 2D images to complex 5D datasets.

Prerequisites

Before starting, ensure you have installed the following software:

• Anaconda: A free and open-source distribution of Python and R for scientific computing, which simplifies package management and deployment.
• Git: A version control system used to manage the source code.

Installation Instructions

Installing Anaconda

Anaconda simplifies package management and deployment for Python/R and is recommended for this course to manage environments and dependencies efficiently.

1. Download Anaconda:

   • Visit the Anaconda Distribution page and download the installer for your operating system.

2. Install Anaconda:

   • Windows:
     • Run the downloaded installer.
     • Choose the install location and ensure that “Add Anaconda to my PATH environment variable” is checked.
     • Complete the installation and restart your computer if required.
   • macOS:
     • Open the downloaded .pkg file and follow the instructions.
     • Ensure that the installer is allowed to install in the desired directory (administrator privileges may be required).
   • Linux:
     • Open a terminal and navigate to the directory containing the downloaded script.
     • Run the script with bash Anaconda3-xxxx.xx-Linux-x86_64.sh (replace xxxx.xx with the version number).
     • Follow the on-screen instructions during the installation.

Cloning the Repository with Git

To download the course materials, you will need to clone the repository using Git.

1. Install Git (if not already installed):

   • Windows/Linux/macOS: Download from Git SCM and follow the installation guide for your OS.

2. Clone the Repository:

   • Open a terminal or command prompt.
   • Navigate to the directory where you want to store the course materials.
   • Run the following command:

   git clone https://github.com/rmsreis/NUANCE_TechTalk_2024.git