IMOD Segmentation Files

IMOD is a suite of programs for processing and analyzing data from electron microscopy and tomography. IMOD binary files contain segmentation mesh data and contour data. They can be opened in many ways, like other registered file types. The IMOD file type can be indicated with a suffix (.imod or .mod, part of the filename) or a prefix (imod:, not part of the filename).

By default, only the mesh data are read and displayed. The contour data are not read by default because creating contours is slow, but reading such data can be enabled as described below. Mesh data are displayed as models of the same type as created by Volume Viewer. The mesh for each object in the IMOD file becomes a separate surface group in a single Chimera surface model and is colored as indicated in the IMOD file. A surface model can be selected for accelerator actions. IMOD surfaces are not saved in sessions.

By default, hovering the mouse cursor over a segmented object (without clicking any buttons) will show the name of the object. This atomspec balloon behavior can be turned off in the General preferences.

See also: Color Zone, Measure and Color Blobs, Surface Color, Surface Zone, mask

Contour Data

To enable reading contour data, it is necessary to modify the code: in the file share/IMOD/, change "contours = False" to "contours = True" and restart Chimera. IMOD contour lines and points will then be read and shown as Volume Tracer markers and links. A separate marker set will be generated for each IMOD object that has contours.

UCSF Computer Graphics Laboratory / February 2008