Particle Stack Editor

Access: CP::Editor::PTK

The main function of the PTK-Editor is for particle stack display, browsing, editing and 2D image processing.

Example of the CP and DP display for the Particle Stack Editor (with particle selection).

Display a Particle Stack

The data input/output functions are organized in the File group (at the upper-left region of the page).  Once a particle stack is loaded into the editor, the image frames will be displayed as a montage in DP::MainDisplay.  The filename, frame & stack dimension and pixel size (modifiable, assumed to be isotropic) will be shown in the designated value-boxes.  A set of functional buttons on top of the filename box control the data I/O:

• : open a file browser to select and load one particle stack into the editor.
• : prompt for a filename to save the particle stack in the editor.
• : display the image statistics (in CP::MessageBoard) of the particle stack.
•  C : close the stack in the editor and clear the display.  Will prompt to save if the stack has been modified.

Browse a Particle Stack

Upon launching the Particle Stack Editor, an associated toolbox in DP::ToolBar will be switched on, which contains the following buttons and value-boxes for stack browsing:

• : to the beginning of the stack display.
• : one page backward in the stack display (keyboard shortcut: PageUp).
• : one page forward in the stack display (keyboard shortcut: PageDown).
• : to the end of the stack display.
• : toggle the frame sequential ID display (the index starting at "1").
• To jump to a particular particle image, enter its frame ID in the yellow value-box and press Enter.
• A count of selected particle images (in blue mask) is displayed in the value-box (gray) on the right.
• C : clear the particle image selection and reset the selection counter.

Select Particle Frame(s)

A particle in the editor can be selected or deselected by the keyboard/mouse combination CTRL+LeftClick while placing the mouse cursor over the target image.  The operation is accumulative and can proceed in any order.  To select or deselect a series of particles, use the range-selection function (with value-boxes and buttons) in the Display Parameter group.  The display quality (Normal, Fine & Super) and display scale (an integer factor) can be customized at the user's discretion.  The Display button in the group refreshes the graphical content in DP::MainDisplay.

Edit a Particle Stack

A set of buttons (at the lower-right region of the page) provides functions for stack editing (on selected frames):

• : build a new stack from the selected frames.
• : open and append another stack to the existing stack in the editor (no particle selection is required).  The two stacks should have the same frame dimension and pixel size.
• : build a new stack that excludes selected frames.
• : close the stack file and clean up the display window (prompting to save the stack, if modified).

Image Processing Functions

Most of the functions in the pull-down menu are designed to process each particle image and loop through all the frames in the stack.  After selecting a function and setting its associated parameters, press the Apply button to activate the image-processing function.  Upon successful completion, the stack display will be updated in DP::MainDisplay to reflect the result.

• Normalization : pixel value is normalized to N(0, 1).
• Intensity Scaling : each pixel value p is modified to (k*p+b).  For example, (k=-1, b=0) inverts the image contrast.
• TopHat Filter : filter each frame by a box kernel centered in the frame.  Size is in pixels.
• Gaussian Filter : filter each frame by a Gaussian kernel.  Sigma is defined by a ratio to the Nyquist frequency.
• Band-pass Filter : filter each frame by High-pass & Low-pass frequency thresholds (in Å, with soft edges).
• Sharpening Filter : sharpen each frame by a reversed Gaussian filter.  Sigma is a ratio to the Nyquist frequency.
• Intensity Clipping : clip pixel intensity according to the specified Min & Max thresholds.
• Cropping / Padding : crop or pad each particle frame (from the center) to the dimension New X/Y.  In padding, the average intensity of the stack will be used to fill the empty space.
• Frame Resampling : resample each frame to the specified new dimension New X/Y using bilinear interpolation.
• Particle Sum : pixel-wise add all particle images into one frame.
• Particle Binning : isotropically bin image pixels by the factor Bin Size.  Integer arithmetics (e.g., 9/2=4) is used to calculate the new dimension.
• Particle Sinogram : calculate a sinogram for each particle at the specified Ang-Step (angular step) & Mask Radius (circular).
• Particle Centering : center each particle in its frame by applying the translation of alignment.
• Rotational Ave : rotationally average pixels of each frame.
• Rotational Sum : rotationally average the "Frame Average", resulting in a single frame.
• Rotation : rotate each frame by the specified angle ("+": counter-clockwise, "–": clockwise).
• UDF Plug-in : call the User Defined Function.

The stack editing and image processing functions will change the value of image pixels and will update the montage display in the PTK-Editor.  However, the resulting stack is not automatically saved back to the original file.  It is at the user's discretion to export the result to a stack file.  As a safe-guard, PARTICLE will prompt to save any modified stack upon its closing.