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executable file
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% TOM Toolbox
% Version 1.99
%
% Acquisition
% tom_tilt_series Tool to acquire a tilt series (WDN & FB).
% Note: sub-functions are not listed. See Acquisition folder or documentation
%
% Analysis
% tom_ccc calculates normalized 3d cross correlation coefficient (FF)
% tom_cm calculates the center of mass (1D, 2D, 3D, AL)
% tom_corr computes 3d cross correlation fuction (FF)
% tom_create_ctf calculates 2D or 3D CTF (pure phase contrast) (2D, 3D, FF)
% tom_ctf calculates and plots CTF (pure phase contrast) (1D, FF)
% tom_ctf_zero calculates zeros of CTF (pure phase contrast, FF)
% tom_dev calculates deviation etc. for images (2D, 3D, AF, tested FF)
% tom_hist3d calculates a histogram of 3D data(SN)
% tom_moi calculates the moments of inertia (3D, FF)
% tom_orcd performs three-dim. orientational search (FF)
% tom_peak determines the maximum/minimum value (1D, 2D, 3D, AL & GS, tested FF)
% tom_xraycorrect corrects X-Ray defects on EM-Images (2D, AL)
% tom_compare compares 2 arrays in Fourier space (2D, 3D, MR)
% Average 2D
% tom_av2_particlepickergui tool for 2D averaging of single particles (WDN & FB)
%
% Average 3D
%
%
% Display
% tom_ctffit tool to determine the defocus (2D, WDN)
% tom_dspcub visualization of a 3D volume in a gallery (3D, AF)
% tom_embrowse browser for EM files (2D,3D, WDN)
% tom_imagesc similar to imagesc, transposes the image (EM style)(WDN)
% tom_intervol visualization tool for 3D data loaded in memory (3D, WDN)
% tom_isosurface tool for isosurface representation (SN)
% tom_particles tool for interactive 3D particles picking (3D, WDN, tested SN)
% tom_picker tool for interactive 3D particles picking loaded in memory (FF)
% tom_volxy visualization tool for 3D volumes (SN)
%
% Filtering & Transformation
% tom_bandpass performs bandpass filtering of image or volume (FF)
% tom_cut filtering in Fourier Space (AL)
% tom_filter convolutes with spherical or quadratic kernel (FF)
% tom_fourier calculates the fourier transformation of an image (1D, 2D, 3D, AL, tested FF)
% tom_ifourier calculates the inverse fourier transformation of an image (1D, 2D, 3D, AL, tested FF)
% tom_laplace performs Laplace filtering of image or volume (FF)
% tom_oscar performs 3D cross correlation of template and volume (FF)
% tom_ps calculates power spectrum of an image (2D, 3D, FF, tested FF)
% tom_shift shifts image by a vector (even subpixels) (1D, 2D, 3D, FF)
% tom_smooth performs smoothing of borders (2D, 3D, FF, tested FF)
% tom_smoothz performs smoothing of borders along z only (2D, 3D, FF, tested FF)
% tom_wedge calculates wedge - to be used as a filter for tomo (3D, FF)
% tom_weight3d weighting function for tomographic reconstruction (FF & FB)
%
% Geometrical shapes
% tom_circle generates a circle (AL)
% tom_cylinder creates an 3D array with a cylinder inside (SN)
% tom_cylindermask masks volume with (fuzzy) cylinder (3D, FF)
% tom_ellipsemask masks volume with (fuzzy) ellipse (3D, FF)
% tom_sphere creates volume with a sphere (FF)
% tom_spheremask masks volume with (fuzzy) sphere (2D, 3D, FF)
%
% Input/Output functions
% tom_convert converts images to a different file format (AL & GS)
% tom_emheader Adds a EM-header structure to a matrix (SN)
% tom_emread reads data in EM-file format (SN)
% tom_emreadc reads data in EM-file format. Developer version !(SN)
% tom_emwrite writes data in EM-file format (SN)
% tom_emwritec writes data in EM-file format. Developer version !(SN)
% tom_isemfile checks if data is in EM-file format (SN)
% tom_ismrcfile checks if data is in MRC-file format (SN)
% tom_mrcreadclassic reads data in MRC-file format (SN)
% tom_mrcstack2emseries converts a MRC-file format stack in a series of single EM-files (SN)
% tom_mrcstack2emstack converts a MRC-file format stack in a EM-format stack (SN)
% tom_mrcwriteclassic writes data in MRC-file format (SN)
% tom_pdb2em Converts PDB-files to EM files (SN)
% tom_pdbread reads a Protein Data Bank (pdb) file into a MATLAB structure (SN)
% tom_rawread user interface for reading raw data (SN)
% tom_reademheader reads only the header of an EM-file (SN)
% tom_readmrcheader reads only the header of an MRC-file (SN)
%
% Miscellaneous
% tom_error generates Gaussian or Poisson noise (AL)
% tom_makemovie generates an avi-file format movie file from a 3D stack (SN)
%
% Reconstruction
% tom_backproj3d performs 3D backprojection (SN)
% tom_rec3d a tool for tomographic 3D reconstructions (WDN)
% tom_reconstruction3d performs an aligned, weighted backprojection (SN & FB)
% tom_recparticles to reconstruct particles with high resolution, from tom_particles (3D, WD, tested SN)
% tom_setmark tool for the alignment of projections (2D, WDN, tested FF)
%
% Spatial Transformation
% tom_bin performs binning of 1D, 2D or 3D images (1D,2D,3D , FF, tested SN)
% tom_cart2cyl transforms 3D-volumes from cartesian to cylinder coordinates (FF)
% tom_cart2polar transforms 2D-images from cartesian to polar coordinates (2D, FF)
% tom_cart2sph transforms 3D-volumes from cartesian to spherical coordinates (3D, FF)
% tom_cyl2cart transforms 3D volume from polar to cartesian coordinates(FF)
% tom_limit sets limits to the values of an image (2D, 3D, AL)
% tom_mirror creates the mirror of an image (2D, 3D, AL)
% tom_move moves the image in x,y,z direction (2D, 3D, AL, tested FF)
% tom_paste pastes array a into array b (AL)
% tom_pointrotate rotates a 3D vector point (FF)
% tom_polar2cart transforms 2D-images from polar to cartesian coordinates (2D, FF)
% tom_red extracts a subimage/subvolume from the input image/volume (AL)
% tom_rotate rotates a 2D or 3D data (3D, SN & FB)
% tom_sph2cart transforms 3D-volumes from polar to cartesian coordinates (3D, FF)
% tom_symref does n-fold symmetrization of a 3D reference (3D, FF)
%
% Utilities
% tom_chooser subjective classification of particles based on a motive list (3D, FF, tested FF)
% tom_sortseries copy, correct x-rays and sort a tiltseries by angles (SN)
% tom_tilt_lines plots marker points (FF)
%
% To Do:
% tom_proj3d2d
% tom_phantom3d
% tom_proj3d2d
% tom_mrc2em
% tom_mrcread reads data in MRC-file format, FEI style (SN)
% tom_spiderread reads data in SPIDER-file format (SN)
% tom_infoseries
% tom_imadj
% tom_symref2d does n-fold symmetrization of a 2D reference (2D, FF)
% tom_tiltstrech
% tom_unbend
% tom_crowther tool for estimating the resolution with the s.c. Crowther criteria (SN)
% tom_average3d
%
%
% Installation
% makefun compiles Functions (please extend after creation of Functions ...)
%
% Electron Tomography toolbox of the
% Max-Planck-Institute for Biochemistry
% Dept. Molecular Structural Biology
% 82152 Martinsried, Germany
% http://www.biochem.mpg.de
%
% Copyright, 27/11/02
% Last changed: 30/04/04
%
%
%