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
Target Audience
Assumed knowledge of Atomic Force Microscopy and the steps involved in processing images such as...
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
pwd/cd)ls)cp/mv).Conda basics (activate topostats env)
Configuration File Understand the Configuration File
Stretch goal of plotting grainstats????