Scripts

Scripts are the main point of user-interaction with the processing pipeline. As such care has been taken to make sure that the scripts are well commented and that the user-defined options are well separated from the actual black-box level processing further down in the code.

Each script is a simple BASH file that generally calls some piece of code from either IMOD or a subTOM Matlab function. The scripts are meant to be first edited, filling in the necessary information and then executed in the terminal. Matlab is not necessary to run the scripts, just the Matlab Compiler Runtime, which should have been taken care of in the installation.