====== Stacks ====== **This submenu contains commands that work with stacks.** ==== Add Slice ==== Inserts a blank slice after the currently displayed slice. Hold down the **Alt** key to add the slice before the current slice. ==== Delete Slice ==== Deletes the currently displayed slice. ==== Next Slice ==== Displays the slice that follows the currently displayed slice. As a shortcut, press the ">" key. ==== Previous Slice ==== Displays the slice that precedes the currently displayed slice. As a shortcut, press the "<" key. ==== Set Slice... ==== Displays a specified slice. The user must enter a slice number greater than or equal to one and less than or equal to the number of slices in the stack. (Slices start at "1"). ==== Images to Stack ==== Creates a new stack consisting of all images currently displayed in separate windows. The images must all be the same type and size. ==== Stack to Images ==== Converts the slices in the current stack to separate image windows. ==== Stack to Hypervolume... ==== Converts a stack to a Hypervolume with third and fourth dimensions. ==== Hypervolume to Stack... ==== Converts a Hypervolume back into a stack of slices. ==== Make Montage ==== Produces a single image which contains the images from a stack displayed in a grid format. This can be useful for visual comparisons of a series of images stored in a stack. A dialog box allows you to specify the magnification level (**Scale Factor**) at which the images are copied, and to select the layout of the resulting grid **(Colums,** **Rows**, **First Slice**, **Last Slice**, **Increment**). With ImageJ 1.35m or later, check **Use Foreground Color** to draw borders and labels in the foreground color and to fill blank areas with the background color. Use the //Montage Shuffler tool macro// to reorder the images in the montage. ==== Reslice... ==== Reconstructs one or more orthogonal slices through the image volume represented by the current stack. Before using this command, create a straight line or rectangular selection to specify were the reconstructions will be done. A dialog box allows you the specify the Z-Spacing (displacement between slices) of the source volume. Multiple slices are reconstructed and saved as a stack if you create a rectangular selection or set Slice Width greater than one. Images are created by sampling each slice in the stack along the line. Thus, the first pixel in each row of the output image is taken from the start of the line and the last from the end. In the case where Slice Width is greater than one, a stack is created by shifting the line down and to the left to generate additional slices for the output stack. This plugin, and the //ZProject plugin//, were contributed by Patrick Kelly and Harvey Karten of the University of California, San Diego. ==== ZProject... ==== Projects an image stack along the axis perpendicular to image plane (the so-called "z" axis). Six different projection types are supported. The ZProject command creates image names in the form "XXX_stack", where XXX is "AVG", "MAX", "MIN", "SUM", "STD" and "MED" and "stack" is the name of the stack.\\ **Average Intensity** projection outputs an image wherein each pixel stores average intensity over all images in stack at corresponding pixel location. Maximum Intensity projection (**Max**) creates an output image each of whose pixels contains the maximum value over all images in the stack at the particular pixel location. Minimum Intensity projection (**Min**) creates an output image each of whose pixels contains the minimum value over all images in the stack at the particular pixel location. **Sum Slices** creates a real image that is is sum of the slices in the stack. **Standard Deviation** creates a real image containing the standard deviation of the slices. **Median** creates an image containing the median value of the slices. ==== 3D Project... ==== Generates an animation sequence by projecting through a rotating 3D data set onto a plane. Each frame in the animation sequence is the result of projecting from a different viewing angle. To visualize this, imagine a field of parallel rays passing through a volume containing one or more solid objects and striking a screen oriented normal to the directions of the rays. Each ray projects a value onto the screen, or projection plane, based on the values of points along its path. Three methods are available for calculating the projections onto this plane: **Nearest Point**,** Brightest Point**, and **Mean Value**. The choice of projection method and the settings of various visualization parameters determine how both surface and interior structures will appear. This routine was written by Michael Castle and Janice Keller of the University of Michigan Mental Health Research Institute (MHRI). [insert image Dialog] Select **Nearest Point** projection to produce an image of the surfaces visible from the current viewing angle. At each point in the projection plane, a ray passes normal to the plane through the volume. The value of the nearest non transparent point which the ray encounters is stored in the projection image. **Brightest Point** projection examines points along the rays, projecting the brightest point encountered along each ray. This will display the brightest objects, such as bone in a CT (computed tomographic) study. **Mean Value** projection, a modification of brightest-point projection, sums the values of all transparent points along each ray and projects their mean value. It produces images with softer edges and lower contrast, but can be useful when attempting to visualize objects contained within a structure of greater brightness (e.g. a skull). **Slice Spacing** is the interval, in pixels, between the slices that make up the volume. ImageJ projects the volume onto the viewing plane at each **Rotation Angle Increment**, beginning with the volume rotated by **Initial Angle** and ending once the volume has been rotated by **Total Rotation**. The **Lower** and **Upper Transparency Bound** parameters determine the transparency of structures in the volume. Projection calculations disregard points having values less than the lower threshold or greater than the upper threshold. Setting these thresholds permits making background points (those not belonging to any structure) invisible. By setting appropriate thresholds, you can strip away layers having reasonably uniform and unique intensity values and highlight (or make invisible) inner structures. Note that you can also use Image/Adjust/Thresold to set the transparency bounds. \\ Sometimes, the location of structures with respect to other structures in a volume is not clear. The **Opacity** parameter permits the display of weighted combinations of nearest-point projection with either of the other two methods, often giving the observer the ability to view inner structures through translucent outer surfaces. To enable this feature, set **Opacity** to a value greater than zero and select either **Mean Value** or **Brightest Point** projection. Depth cues can contribute to the three-dimensional quality of projection images by giving perspective to projected structures. The depth-cueing parameters determine whether projected points originating near the viewer appear brighter, while points further away are dimmed linearly with distance. The trade-off for this increased realism is that data points shown in a depth-cued image no longer possess accurate densitometric values. Two kinds of depth-cueing are available: **Surface Depth-Cueing** and **Interior Depth-Cueing**. **Surface Depth-Cueing** works only on nearest-point projections and the nearest-point component of other projections with opacity turned on. **Interior Depth-Cueing** works only on brightest-point projections. For both kinds, depth-cueing is turned off when set to zero (i.e. 100% of intensity in back to 100% of intensity in front) and is on when set at 0