Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells FINDSECTION(1) FINDSECTION(1) NAME findsection - Locates section boundaries in tomogram slices SYNOPSIS findsection DESCRIPTION FINDSECTION analyes groups of slices from a tomogram, detects the boundaries of the section, and recommends how much to change tilt angles to make the section flat, how much to shift the tilt axis in Z to produce centered slices, and how thick to make the slices. It can also recommend how much X-axis tilt is needed to make the section flat in the orthogonal direction as well. The program detects the section boundary at a certain position in the tomogram by measuring the standard deviation of image intensity at each value of Y in the tomogram slice. It measures S.D. in a "patch" with a width in the X direction and extent in the Z direction specified by the user. To find the bottom edge of the section, it takes the mean S.D. over several Y values at the bottom of the slice and over Y values just below the middle of the slice. It finds the point where S.D. rises above halfway between these mean values and fits a line to the nearby S.D. values. The Y values where this line crosses the halfway point and the mean at the bottom of the slice are estimates of the position of the middle and the end of the edge, respectively. The mid-positions are fairly accurate and are used to determine the midpoint of the section in Y; the end positions are less accurate and are used just to obtain a more conservative measure of section thickness. The same procedure is used on the top of the section. This analysis is performed at a series of patch positions across the width of the tomogram. It can be done over a set of files (each being a portion of the same tomogram), with the same patch positions being analyzed in each. After analyzing a set of patches for one file, the program determines what rotation is required to make the section be flat. It reports the upward shift needed to center the section in Y, and the slice thickness needed to contain either edge middles or edge ends. These values are derived and reported before and after the recommended rotation is applied. Thickness values are rounded up to integers suitable for taking 3D FFTs. After all files are analyzed, the program makes the same analysis and report based on the data from all of the files. It then computes an X-axis tilt and reports thickness and rotation if that tilt is taken into account as well. Entries to the program: Width of patch in X, number of patches to analyze across the width of the tomogram Number of points to average to get mean S.D. at the edge of the slice, number to average to get mean S.D. near the middle of the slice, and number of points to fit the line to. Note that the within-section average is taken on one side of the middle, not across the center of the slice, so the number of points should be constrained accordingly. Defaults are 3, 10, and 4. Spacing between tomogram samples (the distance in Y in the tilt images.) If a non-zero number is entered, the program will compute the tilt around the X-axis that will make the tomogram be flat in its Z dimension. Number of files to analyze For each file, first enter the name of the file. Then enter the starting and ending slices to analyze (/ for all in the file) Then enter a list of patches to drop from the analysis for that file, or Return to retain all patches. HISTORY Written by David Mastronarde, November 1995 2/18/99: added X axis tilt output