ROBEM is a general purpose imaging program to perform boxing and general 2D visualizations of 3D MAPs. All input and output files to/from this program use the Purdue Image Format (.PIF). Input may be scanned images, boxed images or 3D maps. Output is boxed images or 3D maps.

ROBEM can be used for boxing scanned images. A scanned image is read into the program and either manual or automated boxing methods are used to distinguish individual particles (or "boxes") to the computer. Boxes can be painted with background to eliminate sources of noise.

ROBEM can be used to view a 3D Map of data. Views of the maps can be displayed in planar sections, depth cued images, surface shaded depth cued images, radially cued images, surface shaded radially-cued images or radial projection images. Stereo views of the above may also be obtained. Movies are generated based on the number of frames desired and the permutation of the surface density, light angle, fraction of shading, angles of tilt in either the X or Y direction and min or max radii. The map may be cut to any desired subset of the original and/or "unblobbed" where density islands or "blobs" not touching the main virus density is removed based on certain parameters.

ROBEM can be used to display and manipulate the FFT of images. One may estimate the CTF of the image based on its FFT, perform lattice refinement for the FFT of a crystal image or measure the FFT of the image electronically. CTF estimation and lattice refinement of the FFT can also be used to perform back-calculations to show the effects of lattice filtering or applying a CTF to the data.

Binaries are located in: /usr/local/baker (if available)