Visual Scripting

Access: CP::Visual Scripting and CP::MenuBar::Scripting

In single-particle EM reconstruction, the particle data comes from a large number of micrographs and the task of image processing frequently entails operations repeated over a group of similar objects (e.g., micrographs and stacked particles).  Take, for example, building a particle stack from a set of micrographs.  Conceptually, the workflow may proceed as follows:

1. Open one micrograph, in which:
2. Identify particles by computational template-matching;
3. Determine CTF parameters for the micrograph;
4. Assign the CTF parameters to each particle in the image;
5. Repeat step #1 to #4 for each data micrograph;
6. At the end, group all particles into one particle stack.

PARTICLE has the ability to "learn" an image processing procedure from one instance and then applies the protocol to other objects in the group.  The function can be accessed from CP::Visual Scripting (to record and run) and CP::MenuBar::Scripting (to edit).  In the above example, a script for the steps from #1 to #4 can be created in real-time by recording the sequence of GUI operations on one micrograph.  Then, this script can be automatically executed over the selected micrographs in the project space.  Upon completion, all the identified particles can be grouped into one stack for the subsequent classification and 3D reconstruction.

Create & Run a Script

Similar to a media player, the CP::Visual Scripting group is equipped with functional buttons for:

• Recording mode: activate the button to record a GUI procedure, or de-activate the button to stop the recording.
• Step-play mode: run ONE selected command (mouse LeftClick to highlight) in the script, then wait for further instruction.
• Play mode: apply the script to ONE selected data entry in the DataView spreadsheet, starting from the high-lit command in the script.  The script execution will continue till the end.
• Batch processing: sequentially apply the full script to all active entries in the DataView spreadsheet.

Script Editing

Miscellaneous editing functions can be accessed from CP::MenuBar::Scripting.  These functions can be used during a script recording or for post-editing.

• Open : select and load a script into the script editor.
• Save : export the script in the editor to a file.  The default extension of the script files is "cmd".
• Edit : open an editor to display and modify the entire script.
• Clear : clear the procedure list in the editor.  Will prompt to save if the script has been modified.
• Undo : delete the last command entry in the script.

MenuBar::Scripting::Edit opens an editing page to display a script that contains both the commands and parameters.  In Script Editor on the left, an expert user can directly modify the commands and the associated parameters in the script: the Edit button initiates the editing, which will then turn to Accept for conclusion.  In the Command Parameters group on the right, an individual command (mouse LeftClick to select from CP::Visual Scripting) and its parameters are displayed, which can then be modified and updated to the script by the Confirm button.  PARTICLE will prompt to save a modified script upon its closing.