Once the images are imported, they are listed in the “Project Library” tab. Manual processing allows to fine tune the parameters for these images.

The image to be processed can be opened from the “Project Library” by double clicking the row associated with it in the table. This opens the image in the “Process” tab. Each image opened this way can be accessed from the tab bar. The execution container which is opened looks like below.

The execution container can mainly be divided into four different panels:

Scripts panel contains all available scripts. The processing functionalities provided by Focus are programmed in task-specific scripts. The range of available scripts offered to the user depends on the mode Focus is operated in. Each script calls a few executables (external or internal) and fetches parameters associated with the project or the image from the configuration files as required. Any external executable used (such as, e.g., CTFFIND4) has to be separately installed on the system, and the install location of that executable has to be indicated in Focus only once.

The parameters panel contains all the parameters related to the selected script from the “Scripts panel” are shown in this panel. Things to note:

• More help on a parameter can be obtained by hovering on the label of the parameter
• A globe mark near the parameter means that this parameter is GLOBAL. Changing this parameter will change it on all images
• The lock button can lock or unlock a parameter so that it cannot or can be changed both by the scripts and displayed form
• An arrow icon at the end leads to an external link for extra help

Output of the executed script is provided in this panel. The verbosity of how much output is produced can be changed using the slider of the top right of the panel.

The results container contains the output values and images after the processing is done. Note that:

• The images panel contains physical files which can be opened by double clicking that image.
• A preview is displayed in the bottom panel for the selected image in the image panel

Follow the procedure below to process:

1. Select the script to be processed
2. Change the parameters if required
3. Click the “Run” button on the top right button panel