Software
Software is developed in the laboratory to solve computational problems associated with image analysis and to carry out necessary calculations. If you are interested in any of these programs, please contact John Rubinstein (john.rubinstein@utoronto.ca). Most of these programs require that the MRC image2000 library has been installed. To obtain the MRC suite, contact Jude Short (jms@mrc-lmb.cam.ac.uk) at the MRC Laboratory of Molecular Biology in Cambridge, U.K.| • f90c.com | Compile Fortran 90 programs and link to the image2000 libraries and fftw |
| • f77c.com | Compile Fortran 77 programs and link to the image2000 libraries |
| • build_fspace.f90 | Fast 3-D reconstruction in Fourier space (given Euler angles and shifts) sinc function interpolation |
| • ctfcorrect_class.f90 | Correct a class-average for the CTF by weighting of particles contributing to the class-average as described in Rubinstein et al., 2003 |
| • ex-copy.f90 | Exclusive copy for MRC image stacks (i.e. copy all of the images in a stack into another stack except for the specified images) |
| • genproj.f90 | Generate projections of a 3-D model by interpolation in Fourier Space. Use orientation parameters from a Frealign parameter file |
| • genproj_even.f90 | Generate projections of a 3-D model by interpolation in Fourier Space. Use phi, theta, and psi values that evenly cover the surface of a sphere |
| • inc-copy.f90 | Inclusive copy for MRC image stacks (i.e. copy only the specified images in a stack into another stack) |
| • joinlist.for | Join two or more MRC image stacks interactively or by specifying in a list the names of the files to be joined |
| • mapmanip.f90 | Perform Eularian rotations, magnify or shrink, crop or threshold |
| • realclass.f90 | Helps identify mirror-pairs in a group of class averages |
| • reflect-y.f90 | Reflect a particle or stack about the y-axis |
| • reflect-z.f90 | Reflect a particle or stack about the z-axis |
| • renumberparfile.f90 | Replace the particle numbers in a parameter file so that they run in sequence |
| • rotan.f90 | Rotational analysis software (see Baker and Rubinstein, 2008) |
| • rotateimage.f90 | Rotate a 2D image or stack by a specified angle |
| • subavefromeach.f90 | Preliminary processing step for rotational analysis |
| • tiltaxis_mrc.f90 | Determine orientation and angle of tilt between two images |
| • totsum.f90 | Add all of the images in a stack to form a single image |
Ab inition resolution determination: R-measure
http://emlab.rose2.brandeis.edu/rmeasure
Analysis of 2-D crystals: 2DX
http://2dx.org
Compiling Fortran90: Intel Fortan90 Compiler
http://software.intel.com/en-us/intel-sdp-home/
Fourier Transform subroutines: FFTW
http://www.fftw.org/
Making movies for RotAn: ImageJ
http://rsb.info.nih.gov/ij/
Multivariate Statistics and General Image Manipulation: SPIDER
http://www.wadsworth.org/spider_doc/spider/docs/spider.html
Projection matching and model refinement: FREALIGN
http://emlab.rose2.brandeis.edu/frealign
Rendering: UCSF Chimera
http://www.cgl.ucsf.edu/chimera/