Command: segger

The segger command acts on segmentations created with Segment Map. See also: segmentation, volume mask, save

Export a segmentation model from Segment Map as an index map, a type of volume data in which the value at each grid point is the integer ID number of the segmentation region that contains it, or zero if the point is outside of any regions.

A pathname for saving the map can be specified with savePath. Giving pathname as the word browse opens a file browser window for choosing the name and location interactively. If savePath is not used, the map will be opened in ChimeraX but not saved to a file. The file format can be specified with format (default mrc). 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 given as either a single integer N (number of points in each dimension) or three integers separated by commas only, where Nx, Ny, and Nz are the numbers of grid points in the X, Y, and Z dimensions, respectively.