Chimera Commands Index

segment operation arguments

The command segment acts on segmentation models, which are surface models and associated information from Segger, and segmentation regions, surface pieces within a segmentation model. See also: mask, volume

Possible values of operation:

Each operation keyword has different arguments, described below. Operation keywords and their sub-keywords can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.

Segmentation models, segmentation regions, and volume data sets can be specified by model number (e.g., #1) or as a selection (e.g., sel).

segment copygroups segmodel1 segmodel2
Copy the grouping from one segmentation model (segmodel1) to another (segmodel2). Regions of segmodel2 are grouped together if their maximum-value grid points lie within the same (grouped) region of segmodel1.
segment directioncolor regionspattern circle | circle111 | rgb | rgb111 | rgb2 | cmy | cmy2 | cmz ] [ spherekey true|false ]
Color regions according to long axis direction. The long axis is the principal axis with minimum inertia, calculated with equal weighting of each grid point in the region. Many color schemes (pattern settings) are available for showing the axis orientations within the segmentation model coordinate system. The spherekey option indicates whether a sphere depicting the corresponding color key should be displayed.

See also: scolor, measure inertia, Render by Attribute

segment exportmask segmodelsavePath path ] [ format mrc | dsn6 | cmap | netcdf ] [ sequentialIds true|false ] [ binSize bi,bj,bk ]
Export a segmentation as an integer-valued density map in which the value at each grid point is the ID number of the segmentation region that contains it. A location and filename for saving the map can be specified with savePath, and the file format specified with format (default mrc). If no savePath is given, the map will be opened in Chimera but not saved to a file. Segmentation region ID numbers are often nonsequential. If sequentialIds is true (default), the regions will be renumbered starting from 1 in the created map; otherwise, the original ID numbers will be used. By default, the map will be the same size as the map that was segmented. If the segmentation was done on a binned map, however, the binSize option is useful for exporting to the original, unbinned size.
segment sliceimage regions volumetraceSpacing  spacing ] [ traceTipLength tlength ] [ unbendSize size ] [ unbendYAxis x,y,z ] [ unbendGridSpacing g ] [ sliceSpacing sx,sy,sz ] [ xyTrim trim ] [ panelAspect a ] [ imageSpacing pixels ] [ showImage true|false ]
Create a montage image containing slices of unbent segmentation regions along three orthogonal axes. For each region, a center-line is computed with the measure spine command, an unbent region of the specified density map is calculated along that line with the vop unbend command, and a montage image is composed of gray-level rendering of slices along the X, Y, and Z axes of the unbent volume. The traceSpacing and traceTipLength parameters control how measure spine spaces points along the center-line, with default values as defined by that command. The unbendSize, unbendYAxis, and unbendGridSpacing options set parameters for vop unbend: The sliceSpacing values are in physical units and determine the spacing of the slice images taken from the unbent volume, with defaults equal to 10 times its grid spacing. The xyTrim parameter is the fraction (default 0.3) of the unbent volume width and height that should be trimmed. It limits the range of slices perpendicular to the X and Y axes. The panelAspect parameter (default 0.5) is the minimum image aspect ratio (width divided by height) for each of the three panels of tiled slice images; it controls the numbers of rows and columns in each panel. The imageSpacing parameter specifies the number of pixels of padding to leave between the three panels (default 20).

By default, the image will be displayed in a separate window with several buttons:

The separate image window can be suppressed by setting showImage to false. The image is assigned as the region attribute named slices and can be accessed from the Region Attributes dialog.

See also: vop tile

segment unbin binseg fulldata
From a segmentation model (binseg) based on a binned volume data set, generate a new segmentation model for the corresponding full volume data set (fulldata).

See also: vop bin, Volume Filter