This module provides functions for image stack display, editing and image processing. It is accessed from menu: Function: Image Stack Editor.

Image Stack Display & Editing

New: Load a new image stack (MRC format).
Add: Append another image stack to the existing one.
Save: Save the image stack in the editor.
Extract: Extract the selected image frames and remove the rest.
Delete: Remove the selected image frames from the editor.
Clear: Clear the image frame selection.

The image stack in the editor can be browsed through the arrow-buttons in the Display Parameters box. Two keyboard short-cuts are defined to facilitate the browsing: "page-up" for the previous page, and "page-down" for the next page. The starting frame of display can be customized at From, and the size of display can be defined at Scale. The image display quality takes one of three levels: "Normal", "Fine" and "Super". The "Normal" quality is recommended for a newly opened image stack. After a new starting frame or another display quality is chosen, click Display to refresh the graphics window. The sequential label of image frames can be toggled by the ID button.

Particle Image Frame & Coordiantes Synchronization

When a set of particles selected from a micrograph is stored into an image stack, the particle selection in the micrograph and the image frames in the stack editor can be synchronized - any "extraction" or "deletion" operation occurred in the editor is reflected in the particle selections overlaid on the micrograph, and vice versa. This function is active when both the micrograph and the corresponding particle stack are opened. Operationally, when a particle selection session completes, save the image stack and open it in Image Stack Editor (or simply press the button ). The system will prompt the user to synchronize whenever the stack is modified. The user can make whatever changes in the particle selection and switch back and forth between the micrograph display and the editor.

Image Processing Functions

Normalization: Normalize each frame of the image stack to N (0, 1).
Intensity Scaling: Image intensity scaling by "k * I + c". A negative value of "k" will invert the image contrast.
Band-pass Filter: Apply a band-pass filtering. Band-limits are in the unit of Å.
Cropping/Padding: Crop or Pad image frame size (no resampling).
Frame Resampling: Resample each image frame of the stack.
Pixel Binning: Crop or Pad image frame size (no resampling).
Rotational Average: Calculate the rotational average of each image frame.
Rotational Sum All: Add up all rotationally averaged images.
Pixel-wise Sum All: Add up all image frames.

Some of the functions require parameter input, which can be defined in the value boxes below. Click the Apply button to activate the function.