The graphical user interface (GUI) of PARTICLE is structured hierarchically in the following order (starting from the root): panels, modules, groups and objects. Upon the program launch, two windows will pop up: the Control Panel (CP) and the Display Panel (DP), which are at the root of the program GUI. CP contains image analysis and data management functions grouped into multiple modules, such as DataView, Micrograph, Particle, and 3D Model. DP handles the task of data visualization in a variety of forms: chart-plot, 2D image, particle stack, 3D density map and PDB structure display.
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Example: the Control Panel (CP) and the Display Panel (DP) of the program GUI.
The building blocks of the program GUI are functional objects such as value-boxes for parameter input, buttons for process activation, and pull-down menus for item selection. For clarity, throughout the user manual, an object will be referenced by a hierarchical nomenclature in the form of:
which uniquely identifies its location in the GUI by the order of panel, module, and functional group. For instance, the notation CP::MenuBar::Project::Open indicates that the function Open (for "Opening a Project Space") can be accessed from the CP panel, the MenuBar module, under the Project menu group. For simplicity, when the higher hierarchies are self-evident from the context, they will be omitted in the specification. So in the above example, in the manual section describing functions at the MenuBar of the CP panel, a short-form of MenuBar::Project::Open or even Project::Open will be used instead.
The architectural design of the program GUI follows the data processing pipeline in single-particle EM structural analysis. Generally, as a project progresses, function calls will move from CP::DataView (data import and management), to CP::Micrograph (image quality evaluation and CTF determination), to CP::Particle (single-particle or tilt-pair annotation), and eventually to CP::3D Model (model reconstruction and evaluation). The user can switch back-and-forth among these major modules, and invoke data editors (IMG, PTK and MAP) whenever necessary.