The Control Panel

The Control Panel (CP) contains data analysis and management functions that are organized into multiple modules such as DataView, Micrograph, Particle, and 3D Model.  An overview of the main modules and groups of CP will be presented as follows, while leaving the details of their functionality to the respective sections in this user manual.


Design overview of the Control Panel (CP), showing the DataView page.


CP::MenuBar

The MenuBar module contains menu groups (Project, Function, Scripting, System) for project management, function access, visual scripting and system setup.

Project : project space management.

Function : miscellaneous utility functions.

Scripting : procedure visual scripting and editing.

System : environment setup and system management.


CP::Editor

The Editor group (next to MenuBar) contains four monitor-shaped buttons that can quickly switch among major data display modes:


CP::Monitor

The Monitor (below the Editor group) can be used to display basic image information such as intensity histogram and power spectrum.  It is also used to display individual particle frame in particle selection and region of interest in image editing.


CP::DataView

The DataView module (see the figure above) contains a spreadsheet that summarizes the most important attributes of the image data in the project space.  Above the spreadsheet, the project name and basic statistics (e.g., image, particle counts) are displayed; below the spreadsheet, a group of menu/button manages the data entry in the project space (import, remove, stack, etc.).


CP::Micrograph

The Micrograph module is composed of two tabs (Micrograph and Imaging Setup), providing functions for 2D-image display, filtering, editing, and micrograph CTF determination & correction.




Micrograph::Micrograph (tab) contains functions for 2D image display and image processing & editing:

Micrograph::Imaging Setup (tab) contains functions for CTF modeling and determination:


CP::Particle

The Particle module contains functions for particle annotation and screening, in both single image (the Single Image tab) and tilt-pair images (the Tilt Pair tab).




Particle::Single Image (tab) provides functions for manual and computational particle annotation in a single micrograph:

Particle::Tilt Pair (tab) provides functions for manual and computational particle annotation in a tilted image pair:


CP::3D Model

The 3D Model module contains multiple tabs for particle alignment, classification, 3D reconstruction and model evaluation.




3D Model::Alignment (tab) provides functions for particle stack alignment:

3D Model::Classification (tab) contains functions for particle classification:

3D Model::Reconstruction (tab) contains functions for EM density map reconstruction:

3D Model::Evaluation (tab) contains functions for model evaluation (resolution, validation, etc.):


CP::Visual Scripting

The Visual Scripting editor (located at the lower-right region of CP) records GUI actions and builds a procedure that can be used for data batch processing.  When the recording is on, each GUI operation (excluding graphics rendering) will be sequentially entered into a procedural script and displayed in the list, until the recording is manually stopped.  Then the same procedure can be applied to each active data entry in the project space for high-throughput batch processing.


CP::MessageBoard

MessageBoard (the large, blue rectangle at the lower left region of CP) displays text output and warning messages during data processing.  Normal messages will be displayed in yellow color, and error messages will be display in red color on both the message board and a pop-up alert window.


CP::?

The Live Help button (located at the upper right corner of CP) turns yellow when activated, becoming ready to provide a brief description for a selected functional object (e.g., value-boxes, buttons) in the GUI.  The help message will be displayed in CP::MessageBoard, introduced by the text "– help –".  Note that when CP::? is active, parameter changes (e.g., input to value-boxes) at the GUI will be accepted, but the actual data processing functions (e.g., activated via buttons) will not be initiated.


CP::SystemStatus

The CP system status indicator (located at the upper right corner of CP) turns green when the program is ready for instruction, and becomes red when it is busy.  There is a synchronized indicator in the DP panel displaying the same system status.

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