Target Audience and Outcome Objectives

[ns-rse]

Target Audience

Assumed knowledge of Atomic Force Microscopy and the steps involved in processing images such as...

• Flattening
• Scar Removal
• Grain Finding
• Masks
• Tracing

Basic familiarity with computers is required but no familiarity with the Command Line Interface, or Conda environments is required, this is the content covered by the course. Python programming is not required as we are teaching users how to use TopoStats. Learning how to use the individual stages (as in existing notebooks) actually requires some Python basics and will, hopefully, be covered in future material that is developed.

Outcome Objectives

After undertaking the course attendees should have an understanding of and be able to perform the following.

Basic command line navigation

• Move to where images are (pwd / cd)
• List files/images (ls)
• Copying/move files (cp / mv).
• Understand how the command line relates to file manager views.

Conda basics (activate topostats env)

• Understand what an environment is
• Create environments
• Activate environments
• Install packages in the environment
• Install TopoStats
• Use terminal to install TopoStats via pip through conda

Configuration File Understand the Configuration File

• Know what each of the basic parameters do in the config file
• Process Images
• Run topostats on a folder of files
• Impact of parameters on images
• Understand what base_dir, output_dir do
• Understand what cores does
• Understand how filters effects images
• Understand how grains effects images
• Understand what core / all does

Stretch goal of plotting grainstats????

• Be able to use a topostats csv file to plot the area of molecules as a kde plot
• Possibly do this for two datasets?