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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.


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.


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<n 100 (i.e. (100-n)% of intensity in back to 100% intensity in front). Having independent depth-cueing for surface (nearest-point) and interior (brightest-point) allows for more visualization possibilities.

Check Interpolate to generate a temporary z-scaled stack that is used to generate the projections. Z-scaling eliminates the gaps seen in projections of volumes with slice spacing greater than 1.0 pixels. This option is equivalent to using the Scale plugin from the TransformJ package to scale the stack in the z-dimension by the slice spacing (in pixels). This checkbox is ignored if the slice spacing is less than or equal to 1.0 pixels.

Plot Z-axis Profile

Plots the ROI selection mean gray value versus slice number. Requires a selection.

Start Animation

Animates the active stack by repeatedly displaying its slices (frames) in sequence. Use Stop Animation, or click with the mouse, to stop. Open the Animation Options dialog box to specify the animation speed. More than one stack can be animated at a time. As a shortcut, press the backslash key (“\”) to start or stop animation. In ImageJ 1.38 and later, press alt plus backslash to open the Animation Options dialog.

Stop Animation

Terminates animation of the active stack. As a shortcut, press the backslash key.

Animation Options...

Use this dialog to set the animation Speed in frames per second, set the First Frame and Last Frame (1.38 or later), or to enable “oscillating” animation (Loop Back and Forth). In ImageJ 1.38 or later, you can press alt plus backslash (alt+\) to display this dialog.

gui/image/stacks.txt · Last modified: 2019/04/12 13:13 by

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