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Stacks Menu

Windows to Stack
Stack to Windows
Add Slice
Delete Slice
Next Slice
Last Slice
Make Movie...
Capture Frames
Animate
Average
Make Montage...
Capture Color
RGB to 8-bit Color
8-bit Color to RGB
RGB to HSV
Register
Project
Reslice
Stack Info.
NIH Image Manual

Use the commands in this menu to create or process stacks. Stacks are three dimensional images consisting of two or more "slices". The slices can be consecutive serial sections in a 3D data set, frames in a movie loop, RGB (red, green and blue) channels in a 24-bit color image, or any related set of images. Use the '<' and '>' keys to move through the slices in a stack. The current slice and total number of slices are displayed in parentheses in the title bar. Stacks are displayed in a single window and can be saved to a single disk file using the Save, Save As or Export commands. Most commands in Image , with the exception of Save, Save As, Export and Open, operate only on the current slice. There are, however, macros are available (in the file "Stacks") that operate on all the slices in a stack

Windows to Stack

Converts the set of images currently being displayed in separate windows to a stack. The images must all be the same size. A macro, also called "Window to Stack", is available that works with windows that are not the same size.

Stack to Windows

Converts the currently active stack to windows. A stack with 20 slices would be converted to 20 normal image windows.

Add Slice

Adds a new blank slice to the stack following the currently displayed slice. The maximum number of slices in a stack is 1000.

Delete Slice

Deletes the currently displayed slice. You can use Undo to restore it.

Next Slice

Displays the slice following the currently displayed slice. Note that is not necessary to hold down the command key to use the keyboard shortcut, i.e., you only need to press the '>' key. You can also use the Page Down key on extended keyboards.

Last Slice

Displays the slice before the currently displayed slice. As a shortcut, use the '<' or Page Up keys.

Make Movie

Captures a series of video frames into a stack. Before using this command, you must first create a rectangular selection in the Camera window. The size of this selection determines the width and height of the stack that will be created. A dialog box allows you to specify the number of frames and the capture rate. The capture rate is specified by entering either the inter-frame interval (Seconds/frame ) or the frame rate (Frames/second ). Set the inter-frame interval to zero for the fastest capture rate. After Image has completed recording the movie it will compute the actual frame rate and display it in the Info window. If the computed and desired rates are not the same then the frames were probably captured at uneven intervals. In the case, specify a slower rate, use a smaller selection, or try enabling "Blind" Capture. Type command-period to abort the movie making process.

Check "Blind" Capture to disable screen updates, allowing faster frame capture rates.

Check Buffer Capture to use uses the LG-3's expandable buffer memory to store the frames. When combined with blind movie capturing, this enables capturing at video rates. The software limits the number of frames in a movie to the number which will fit in the LG-3's memory buffer (this is the number of Mb on the LG-3 times two). Note that if there is a lot of memory installed on the LG-3, there must also be a lot of system memory in the Macintosh in order to work with the frames once they are captured.

Select Time Stamp to have the elapsed time of each frame written in the upper left corner of each frame. The elapsed times are also stored in the PlotData macro array. See the "Make Movie and Plot Intervals" macro in "Movie Making Macros" for an example of how to record and process the elapsed times.

Check Use Existing Stack to store the frames in the stack last used by Make Movie instead of in a newly created one.

Triggering can be enabled for only the first frame or for every frame. Check Trigger and First Frame and Image will wait for a mouse press before starting to capture the frames.

The table below shows the maximum frame size for various capture rates when using a Quadra 700, a Scion LG-3, and "Blind" capture mode. Faster Macs should be able to capture larger frames at a given rate. The "Frame Rate vs. Frame Size" macro in "Movie Making Macros" was used to generate the table. The table assumes a 60Hz frame grabber card that captures at a maximum rate of 30 fps, or .033 seconds per frame. A 50Hz (PAL) card captures at a maximum rate of 25 fps, or 0.04 seconds per frame.

      Seconds/frame   Frames/second  Maximum Size
          .067             15        320 X 240
          .1                0        480 X 360
          .133            7.5        600 X 460
          .2                5        640 X 480
          .333              3        640 X 480
          .5                2        640 X 480

Capture Frames

Captures a frame and adds it to a stack each time the mouse button is pressed. Press any key to stop capturing.

Animate

Animates the current stack by repeatedly displaying its slices (frames) in sequence. Holding the option key down causes the screen to be erased to the current background color before the animation starts (or type command-option-'=' as a shortcut). The animation speed is controlled by pressing keys '1' through '9'. 68040 and Power PC based Macintoshes using built-in video provide the fastest and smoothest animation. The right and left arrow keys can be used to single step through the slices. Press the mouse button to stop. Check Oscillating Movies in the Video Control dialog box to get Image to automatically reverse direction at the beginning end of the frame sequence.

Average

Creates an new image that is the arithmetic average of all the slices in the current stack.

Make Montage

Creates a new composite image from the slices in the current stack.

Columns and Rows control the number of columns and rows used in the composite image. Scale Factor determines how the slices in the stack are scaled when they are copied to the composite image. Decreasing the scale factor makes the composite image smaller and reduces the amount of memory required. First Slice and Last Slice specify which slices in the stack get copied to the composite image. Every slice (starting at First Slice ) is copied if Increment is set to one, every other slice if it is set to two, every third slice if it is set to three, etc. Check Number Slices to have the slices in the composite image labeled with the slice number. Use the Font, Size and Style commands in the Options menu (before using Make Montage) to vary the format of the labels. Check Borders to draws borders around the slices. The width of the borders can be varied by clicking on the lines at the bottom of the Tools window. Make Montage normally draws labels and borders in white. You can force it to use black by setting the pixel in the upper left hand corner of the first slice to white (value = 0).

Capture Color

Captures and displays a 24-bit RGB color image. Requires a Scion or Data Translation frame grabber card and an RGB color camera with separate composite sync output. With the Scion frame grabber cards, an optional four channel cable is required and Separate Sync must be checked in the Video Control dialog box. With the Data Translation QuickCapture, the W5 jumper must be installed and the red, green, blue and sync camera outputs connected to cables 1, 0, 2 and 4 respectively. Color capture is very memory intensive.

RGB to 8-bit Color

Converts an RGB color image (in the form of a three slice stack) to 8-bit indexed color. You have a choice of three 256 color look-up tables to use with the indexed color image. Select Existing to use the current look-up table. Select System to use the Apple default 8-bit color table. Select Custom to create a custom 256 color table based on the colors in the RGB image.

Checking Dither causes the 8-bit color image to be drawn using error diffusion dithering, a technique that mixes existing colors to create the illusion of additional colors. Dithering will usually eliminate color banding in the 8-bit image.

8-bit Color to RGB

Converts an 8-bit indexed color image into a three slice (red, green and blue) stack, a format that allows filter operations such as smoothing and sharpening to be performed. Macros are available in the file "Stacks" for automating filtering operations on RGB stacks.

RGB to HSV

Converts an RGB color image (in the form of a three slice stack) to HSV (Hue, Saturation and Value).

Register

Translates and rotates the slices in the current stack into alignment based on fiducial points.

There are two interfaces. The more intuitive of the two requires the user to click on visible landmarks in a reference slice, then click on corresponding fiducial points in the other slices in the stack. The code then lines up the slices based on these points. The user may easily throw out unreliable points in non-reference slices and correct input errors. This registration interface may only be used in cases where all fiducial points are visible on screen in the captured slices.

The second interface is more difficult to use, but it works regardless of whether or not fiducial marks are included within the borders of the captured slices. Here, the user provides fiducial data in a text file. These data consists of relative coordinates of fiducials from each slice as read from a microscope digitizer (or similar device) as well as the necessary information to map the coordinate system of the microscope digitizer to the coordinate system of windows in NIH Image.

The text file method uses relative coordinates of fiducial marks as recorded with some device such as a microscope digitizer. Let us call these coordinates "stage" coordinates. It also uses screen coordinates of fiducials in Image. Before registration may take place, stage coordinates must be mapped to the NIH Image screen coordinate system. To do this, NIH Image reads the following, tab-delimited information from a text file. In every case, x-coordinates are followed by y-coordinates.

line 1: the screen coordinates of a point which is fixed for every image captured. In the sample fiducial file, this is the point which corresponds to the cross hairs on the microscope at capture time. This is the "image center" point.

line 2: the location, in screen coordinates, of two fixed points in an image.

line 3: the location, in stage coordinates, of these same two fixed points.

line 4: (and each subsequent line) the locations, in stage coordinates, of the "image center" and at least two, but nor more than 12, fiducial points for an image to be registered.

Obviously, the stage coordinate system may not change in rotation, translation, or scale in the middle of a set of images being captured, so it is advisable to record stage coordinates at the time of image capture (without changing camera settings or the position of the object whose image is being captured).

Lines 4-n must entered in the same order as the slices in the stack. It doesn't matter which one is the reference image. Where fiducial coordinates are unavailable or unreliable, use the number 10000 for both the x and y stage coordinate in the file. Each slice must be represented by the same number of fiducial coordinates in the data file.

As you can see, using the text file method introduces many possible sources of errors, so results are not usually as good with this method as with the on-screen method.

An example stack with text file fiducial points ('RegistrationExample.bin') is available by FTP from zippy.nimh.nih.gov, in the /pub/nih-image/stacks directory.

This routine was written by Michael Castle (mike.castle@umich.edu) of the University of Michigan Mental Health Research Institute (MHRI).

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 (e-mail: mike.castle@umich.edu) and Janice Keller of the University of Michigan Mental Health Research Institute (MHRI).

Distance Between Slices is the interval, in pixels, between the slices that make up the volume. Image 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 use density slicing to set the transparency bounds.

Sometimes, the location of structures with respect to other structures in a volume is not clear. The Surface 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 Surface 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.

The Minimize Window Size option allows you to save memory by making projection windows as small as possible given the size of the volume and the axis of rotation. If this box is not checked, projection windows for a given set of slices will be the same size regardless of the axis of rotation (convenient for animation sequences using multiple axes of rotation).

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).

Several macros (in the file "Stacks") are available for performing various operations on the slices making up a volume prior to using the Project command. Use "Smooth" to reduce noise in a volume. Since the projection routine assumes volumes contain one or more objects within a black background, use "Invert" to invert volumes with a white background. For low contrast volumes, increase the contrast using the controls in the Map window and then apply the look-up table to the volume using the "Apply LUT" macro. The "Remove 0 and 255" macro changes pixel values of 0 and 255 to 1 and 254 respectively. This is sometimes useful when pseudocoloring projections. Use "Replicate Slices" to eliminate the gaps seen in projections of volumes with a slice interval greater than one by increasing the number of slices. The "Make Cone" macro creates a 643 volume containing a cone with two rods inside that is very useful for understanding the effect of various projection parameters.

Reslice

Reconstructs a 2D image from the image volume contained in the current stack. Use the straight line selection tool to select were the reconstruction will be done. You will be prompted for the slice spacing (displacement between slices in the stack) in pixels if this information has not been previously entered. For experimenting with the Reslice command, a sample MRI volume consisting of 27 5mm slices is available via anonymous FTP from zippy.nimh.nih.gov, in the directory /pub/image/stacks. Macros are available (in the file "Stacks") for repetitive reslicing of image volumes, for example, to generate a set of coronal slices from an MRI volume consisting of sagital slices.

Stack Info

Allows you to view and set the type, slice spacing, and frame interval of the current stack.

A Volume is a stack containing a 3D Image. A Movie is a sequence of frames captured using the Make Movie Command. An RGB Image is a 3-slice stack containing a 24-bit color image in RGB (Red, Green, Blue) format. An HSV Image is a 3 slice stack containing a 24-bit color image in HSV (Hue, Saturation, Value) format. Slice Spacing is the distance between the slices in a volume. Interval is the inter-frame interval in a movie.

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