Summary and Schedule
Welcome to the training material for the TopoStats Atomic Force Microscopy image processing software.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introducing the Command Line | What is a command shell and why would I use one? |
| Duration: 00h 23m | 2. Navigating Files and Directories |
How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer? |
| Duration: 01h 03m | 3. Working With Files and Directories |
How can I create, copy, and delete files and directories? How can I edit files? |
| Duration: 01h 53m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
This course teaches you the basics of using TopoStats to process Atomic Force Microscopy images. TopoStats is software written in the Python programming language so you will need this installed on your system. Most GNU/Linux and OSX operating systems already have Python installed however in order to make a reproducible environment available we will guide you through how to use Conda environments to setup and install an isolated environment for installing TopoStats and its dependencies.
Because of the vast heterogeneity in AFM images we have created a sample data set for you to work through this tutorial with. If time permits at the end of the class you can try processing your own images and instructors may be able to help with any problems that you encounter.
Data Sets
Download the data zip file and unzip it to your Desktop
Software Setup
Conda
Conda is an open-source, cross-platform, language-agnostic package manager and environment management system for the popular programming and data science languages Python and R. For the purposes of this class we will only be using the support for Python.
We ask that you install Conda on your laptops prior to the class so we can maximise the time available for covering the course material. You do not need to worry about creating any Conda environments before the class starts, we cover that as part of the material.
The official installation instructions are comprehensive and detailed and should get you setup.
If you find you are having problems installing the software please contact the instructors for assistance.