![]() This plugin uses the maximum intensity, average intensity, or sum slices projection method to apply a z projection to a stack of images. The Grouped Z Project tool ( Image › Stacks › Tools › Grouped Z Project…) works similarly to Z Project in terms of projection methods. The six projection methods clockwise from top left: average intensity, maximum intensity, minimum intensity, median, standard deviation, and sum slices. These remaining methods also have their distinguishing characteristics, as seen by the median projection which gives the clearest rendering with the trade-off of less of filtering out more of the image in the projection. In the case of the MRI stack, maximum intensity is a preferable method to view the external head rendering while other methods of projection may be used to examine the internal brain components. As seen below, by applying a z transform to an MRI stack using different projection methods, the results can be very different. The appropriate projection type will vary depending on the type of data being represented. There are six different projection types to choose from: average intensity, maximum intensity, minimum intensity, sum slices, standard deviation, and median. The default for these values is the endpoint slices of the stack. When Z Project opens, it prompts for a start and stop slice, which will determine the range of the stack that will be included in the z projection. This process may be used to highlight specific data from the stack and is accessed using Image › Stacks › Z Project… Z Project is a method of analyzing a stack by applying different projection methods to the pixels within the stack. There are several ways to “flatten” the 3D stack. A montage will allow the 3-D dataset to be visualized in 2-D, but results in each frame being very small. ![]() If you’d like to help, check out the how to help guide! Stack-ProjectionsĪ z-series is generally difficult to represent as a 2-D image for publication purposes. Stack.stopOrthoViews - Stops the current Orthogonal Views and closes the "YZ" and "XZ" windows.The content of this page has not been vetted since shifting away from MediaWiki. Stack.getOrthoViewsID - Returns the image ID of the current Orthogonal Views, or zero if none is active. tOrthoViews(x, y, z) - If an Orthogonal Views is active, its crosspoint is set to x, y, z (example). Stack.getStatistics(voxelCount, mean, min, max, stdDev) - Calculates and returns stack statistics. Stack.swap(n1, n2) - Swaps the two specified stack images, where n1 and n2 are integers greater than 0 and less than or equal to nSlices. Stack.getActiveChannels(string) - Returns a string that represents the state of the channels in a composite color image, where '1' indicates a displayed channel and '0' indicates an inactive channel. For example, "101" causes channels 1 and 3 to be displayed. tActiveChannels(string) - Controls which channels in a composite color image are displayed, where string is a list of ones and zeros that specify the channels to display. Stack.getDisplayMode(mode) - Sets the string mode to the current display mode. Requires a multi-channel stack and v1.40a or later. tDisplayMode(mode) - Sets the display mode, where mode is "composite", "color" or "grayscale". tZUnit(string) - Sets the Z-dimension unit. Stack.getUnits(X, Y, Z, Time, Value) - Returns the x, y, z, time and value units. tFrameInterval(interval) - Sets the frame interval in time (T) units. Stack.getFrameInterval() - Returns the frame interval in time (T) units. Stack.getFrameRate() - Returns the frame rate (FPS). tPosition(channel, slice, frame) - Sets the position. Stack.getPosition(channel, slice, frame) - Returns the current position. tDimensions(channels, slices, frames) - Sets the 3rd, 4th and 5th dimensions of the current stack. Stack.getDimensions(width, height, channels, slices, frames) Returns the dimensions of the current image. The HyperStackDemo demonstrates how to create a hyperstack and how to work with it using these functions Stack.isHyperstack - Returns true if the current image is a hyperstack. These functions allow you to get and set the position (channel, slice and frame) of a hyperstack (a 4D or 5D stack). If a macro command is convenient, then please consult the list of commented macro commands
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