software for render 3d stacks and visualize it

The result is a 'height map' showing the focused images. Try “3” for the kernel value in the first instance. The Stack Focuser plugin uses a Sobel edge filter to calculate “best focus”. Grouped Z Project applied to two halves of a stack, resulting in the two slices shown. If group size is set to equal the number of slices in the stack, Grouped Z Project will evaluate the stack in the same manner as Z Project. This is a useful plugin for analyzing large stacks where the change from slice to slice is still relevant, but not all slices need to be examined individually. The result of running this plugin is a new stack where each slice is a a projection of a subset of the original stack. The plugin will then apply the selected projection method to subgroups with this number of slices, starting with the first slice.

Unlike the standard Z Project, this plugin prompts for a group size that must be a factor of the total number of slices in the stack. 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. A z-series is generally difficult to represent as a 2-D image for publication purposes.

Software for render 3d stacks and visualize it