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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.
If the option
key is pressed, then only xy translation, and not rotation, is carried
out. Thus, only one mouse click per slice is required to identify a
reference point that is common to all slices.
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Steve Barrett November 2014 |
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