MRC CAMBRIDGE IMAGE PROCESSING SYSTEM
(Last update: 22-Mar-93)
All documentation in this area is derived from the MRC Laboratory for
Molecular Biology Image package with permission.
The system of image processing programs developed by past and
present members of the Laboratory is used in various forms worldwide
for determining the structure of macromolecular assemblies. The
approach has been to study specimens with some form of symmetry, such
as crystals or helical and icosahedral particles. Programs suitable
for many kinds of 2-D and 3-D analysis have been written. The
philosophy has been to write largely stand-alone FORTRAN programs for
carrying out the various steps of processing. At the present time
(April 1993), there are about 80 stand-alone programs, varying in length
from a few lines to many thousands of lines of code. The unifying
principle has been to use a standard format (MAPFORMAT) for images and
Fourier transforms and a separate standard format (PLOT82) for graphics
files. These are also used in the crystallographic CCP4 system. In
the later stages of some of the procedures, for exmple in high
resolution electron crystallography, amplitudes and phases are put into
a third standard format, that of LCF (labelled column format), which
allows direct access to the X-ray crystallographic software in CCP4.
Libraries of standard subroutines are available for reading, writing and
manipulating files. A user program written to accept files in these
three formats and producing output in the same three formats thus fits
directly into the system, with no need for any modifications to existing
structures. The libraries can be invoked at the linking step on the
Alliant under UNIX or on the VAX under the VMS operating system. We
have produced FORTRAN user codes that will run under either system
without modification.
MAPFORMAT involves each image or transform having an initial
header block 1024 bytes long, which specifies the type and size of the
file, the maximum, minimum and mean densities and information about
origins. Most importantly it also contains a label field which
provides a history of processing operations that have been applied to
the image; the convention is that each program adds a label containing
a one line description of the operation and time of running. More
information about IMAGE format files and the subroutines (IMSUBS) for
manipulating them is given in section 5. Briefly, the IMSUBS routines
are written in FORTRAN and themselves call lower level routines for the
actual reading and writing; these lower level routines are written in C
for the Alliant and in FORTRAN for the VAX. Programs producing
graphical output use PLOT82 routines and the resulting PLT files can
be sent to laserprinter, lineprinter or viewed on a terminal, using
programs which may be installation dependent. Thus apart from getting
digitized data into the system and hard copy out, the system of programs
can be used as a coherent whole, independent of the particularities of
the installation.
3.1 Densitometer programs for digitising images
3.2 General programs for processing micrographs
3.3 2-dimensional crystal processing programs
3.3.1 2d Image analysis
3.3.2 Electron diffraction patterns
3.4 3-dimensional helical programs
3.5 Icosahedral virus programs
3.6 Rotational filtering and averaging programs
3.7 General display programs
4. References to papers which describe these programs
or procedures.
Author: Stephen Fuller
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Last Updated: 15 October, 1995