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.

• New : create a new project space.
• Open : load an existing project space from disk.
• Data : import / delete image data, and set data selection (all, none or reverse) in the DataView spreadsheet.
• Save : export the current project space to disk.
• Close : clear the current project space (will prompt to save if necessary).

Function : miscellaneous utility functions.

• Particle Selection : import particle coordinates from a data file (PTK of Signature, PLT of Imagic or SPD of Spider).
• Particle Attributes : functions to Import / Export / Clear particle (stack) alignment and CTF parameters.
• Selection in Stack : functions to Import / Export / Reverse particle selections in a stack.  The selection is stored in a data file that can be reloaded over the same or a related particle stack.
• Save DP Screenshot : save the graphics content of DP::MainDisplay into a BMP image file.
• Raw Image Loader : import a header-ed image array (2D image, particle stack, or 3D density map).
• UDF Plug-in : set up an user-defined plug-in function (UDF).

Scripting : procedure visual scripting and editing.

• Open : import a script from a file.
• Save : export the script in the editor to a file.
• Edit : open an editor to display and modify a command script.
• Clear : close the script in the editor (will prompt to save if modified).
• Undo : remove the last command entry in visual scripting.

System : environment setup and system management.

• Setup : general system environment and program update.
• About : displaying the package logo and version of release.
• News : a communication channel for news broadcast to the users.
• Exit : terminate the program (will prompt to save the project space whenever necessary).

CP::Editor

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

• IMG : 2D-Image Editor, for micrograph display and editing.
• PTK : Particle Stack Editor, for particle stack display and editing.
• MAP : Density Map Editor, for 3D-map display and editing.
• PDB : PDB Editor, for molecular structure display and editing.

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:

• File group: located at the top-left of the page, including a pull-down menu for image format selection and buttons for file open, save & close.  The information button displays basic image properties (dimension, intensity statistics, etc.).
• Image Processing group: provide frequently used 2D image processing functions in a pull-down menu.
• Notes group: letting the user to record important information about the micrograph (e.g., imaging setup, image quality assessment, etc.).
• Image Property group: provide functions for image histogram and spectrum display (in CP::Monitor).
• Masking group (tab): provide functions for automatic micrograph masking under user-defined variance tolerance.
• Cropping group (tab): provide functions for image cropping, either a rectangular region or a filament along an arbitrary direction.  The cropped region of interest will be displayed in CP::Monitor.

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

• Defocus & Tilt group: define imaging parameters (beam-voltage, pixel-size, nominal defocus, etc.) and solve for the defocus parameters.
• CTF Characteristics group: functions for CTF modeling and display (theoretical CTF, image spectrum, spectrum radial averaging, theory-data comparison, peak contour and fitting zone).
• Refined Parameters group: display refined CTF parameter and imaging tilt geometry.  The Accept button registers the values to the project space.

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 Parameter group: define particle size, image binning factor, and scoring threshold.
• Reference Image group: define reference images (in a stack) for computational screening.
• Load / Save / Clear buttons: load, save and clear the coordinates of particle selections.
• Stack button: box selected particles and group them into one stack, then display the stack in the PTK-Editor.

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

• Image Pair group: open image pair, refine tilt geometry and annotate particle pairs.
• Particle PairList group: list the selected particle pairs.
• Load / Save / Stack buttons: load, save and stack selected particle pairs.
• Inspect button: when toggled on, the selected (high-lit) particle pair in the list will be displayed exclusively for inspection.
• Delete button: delete the selected particle pair from the list.
• Clear button: clear the entire particle-pair list.

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:

• Alignment Parameter group: define alignment method and parameters (filtering, shift-limit, etc.).  The Stat. function summarizes alignment statistics (CC score and in-plane shift) in a chart.
• Alignment Mapping group: relate one set of parameters to another stack (e.g., from binned to non-binned stacks).

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

• Classification Parameter group: define classification method and parameters (filtering, masking, etc.).
• Class Editor group: provide functional buttons for class average and member image editing (extract, delete, etc.).
• Data for Reconstruction group: define the data source for the subsequent model reconstruction (class averages, original particle images, etc.).

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

• Reconstruction Parameter group: define reconstruction method and parameters (ab initio, refinement, symmetry, etc.).
• Refinement Parameter group: define the parameters associated with various methods.
• R-C-T Reconstruction group: dedicated functions for random-conical-tilt model reconstruction.

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

• Basic Functions group: provide frequently used matrices for model quality assessment (re-projection, FSC plot, etc.).
• Tilt Validation group: use particle tilt-pairs for model validation and alignment evaluation.

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.