Version 0.1, 1999-11-30Final release within the framework of the BioImage database project as Bsoft.
- Originating from code developed under the BioImage project including MMIFL
- Oldest code: 19970914 (bgex, bsf)
- Major shift away from SGI-specific code: 19990321 (bimg, rwimg)
- Shift away from the common make utility to the C-shell bmake: 19990814
Version 0.2, 2000-03-30Final release of development at the Biozentrum, Basel.
- Ported to VMS: 20000112
- FFTW and LIBTIFF included in the distribution: 20000303
Version 0.3, 2000-11-01Development starts at the LSBR, NIAMS, NIH, Bethesda.
- Multiple images per file now supported in the reading code: 20000415
- The design for reading STAR format files has been changed: 20000420
- Major reorganization of function names: 20000520
Version 0.4, 2000-12-12Release featured in the paper: Heymann, J. B. (2001). Bsoft: Image and molecular processing in electron microscopy. J. Struct. Biol. 133(2/3), 156 - 169.
Made available through the web server at the LSBR, NIAMS, NIH, Bethesda.
- bcolour: Generates colour images from grayscale images.
- beditimg: Generates/edits images in simple ways.
- bfix: Fixes end-of-line characters for conversion between Unix and Mac.
- bmontage: Generates a montage of 2D images from a 3D image or a multi-image file.
- bsplit: Separates a multi-image image file into single-image files.
Version 0.5, 2001-05-07
- Documentation included (most generated automatically from source files)
- Extensive introduction of geometric manipulations and the use of quaternions.
- badd: Weighted addition of multiple images.
- bbackproj: Real space backprojection.
- bclass: Classifies images with respect to reference maps.
- bfilter: Does a number of filtering operations.
- bmapdist: Determines similarities/differences between images.
- bpartmulti: Compares particle parameters in multiple STAR files.
- bpartsel: Selects particles in a STAR file based on user-specified criteria.
- brandom: Generates random noise images.
- bstar: Edits STAR files.
Version 0.6, 2001-05-27Released at the Gordon conference on 3D electron microscopy in Rhode Island.
- bctf: Determines and applies CTF.
Version 0.7, 2001-11-05Production version update.
- bcomplex: Transforms complex images.
- bmatrix: Matrix operations.
- bmol: Atomic coordinate manipulations (originally bcoor).
- bpick: Picking particles and aligning micrographs (originally bpair).
- bsym: Symmetry operations on images.
- btree: Outputs postscript files from Phylip phylogeny trees.
Version 0.8, 2002-05-27Production version update.
- breconstruct: Fourier space reconstruction from 2D images.
- bsegment: Segments images in various ways.
Version 0.9, 2002-12-20Production version update. Final release of development at the LSBR, NIAMS, NIH, Bethesda.
- Added Digital Micrograph image format (only the 2.x format): 20020619
- Change in function names: 20020711
- int fft_img(fftw_direction dir, Bimage* p) ===> int img_fft(fftw_direction dir, Bimage* p)
- int auto_correlate_img(Bimage* p) ===> img_auto_correlate(Bimage* p)
- Bimage* cross_correlate_images(Bimage* p1, Bimage* p2) ===> Bimage* img_cross_correlate(Bimage* p1, Bimage* p2)
- float* find_shift_between_images(Bimage* p1, Bimage* p2) ===> float* img_find_shift(Bimage* p1, Bimage* p2, int refine_flag)
- Fixed a problem in the function for finding the shift between images by cross-correlation.
- bnad (denoising by non-linear anisotropic diffusion) from code written by Achilleas Frangakis: 20020803
- Changed micrograph structure hierarchy to a new linked list-based hierarchy: 20020826
- new Bproject: replaces Bmg_group; overall structure for a project.
- new Bfield: field-of-view containing focal or tomographic tilt series.
- Bmicrograph: micrograph parameters.
- new Bparticle: replaces arrays of particle parameters in Bmicrograph.
- STAR tags associated with the new micrograph structure hierarchy: 20020826
- _micrograph.id: A string value identifying a micrograph
- _micrograph.field_id: A string value identifying the field-of-view, must be the same for all micrographs in a field, default value is the micrograph ID of the first micrograph in the series.
- _particle.id: A number corresponding to the image number in a multi-image particle file, replaces _particle.number.
- Major change in dealing with defocus: Previously: Minimum and maximum defocus; Now: Average defocus and deviation.
- bshow, a Tcl/Tk script and interface code: 20021015
- Image display
- Picking single particle images from micrographs.
- Fitting the CTF to micrograph power spectra.
- Extracting filaments from micrographs.
- Marking for segmentation.
- Set up for tomographic processing.
- balign: Aligning and adding micrographs of the same field - intended for focal pairs: 20021128
- bproject: A program to calculate sets of projections within asymmetric units: 20021208
Version 0.9.1, 2003-11-28Pre-official version, attempting to achieve all the goals for version 1.0.0.
- bnorm: Normalizing a set of images based on density distribution: 20030411
- Added new Digital Micrograph image format (3.x format): 20030510
- bfind: Finding a template in an image by cross-correlation:
- Introduced long options: 20030605
- Reworked density generation from atomic coordinates, bgex and bsf: 2003 (over several months).
- bmask: Generating image masks.
- Established installation for Mac OS X to allow launching
bshow from the Dock: 20030907
- Major reworking of bshow: 20030907
- Reading and writing of micrograph parameter files for single particle processing and tomography.
- Reorganization of menus and options.
- Changes in CTF determination.
- Marginally useful automatic particle picking.
- Ongoing improvements in determining CTF (bctf).
- dmerge: Program by David Belnap to merge micrographs from
same field: 20030901
- New STAR tags for micrographs to incorporate more electron microscope parameters (Cc, illumination half-angle, etc.): 20030915
- bcrystal: Calculates coordinates for multiple unit cells: 20030928
- bhelix: Dealing with images with helical symmetry: 20031016
- borient: Single particle image orientation finding program:
Version 1.0.0, 2004-01-15First official version, with extensive support for single particle processing for cryo-electron microscopy.
- Introduced generic linked lists: 20031203
- New web documentation layout: 20040115
Version 1.0.2, 2004-04-15
Reorganization of source code.
- Fixed bview.
- bshow: Activate arrows for navigation and autoscaling.
- bpartsel: Fixed reselection
- bcc: Functions to do cross-correlation (used to be in bfft): 20040206
- bbackproj: Fixed weighting: 20040303
- Introduced reciprocal space masks in bresolve, bfind, and
- bproject: Tilt series: 20040413.
Version 1.1.0, 2004-05-11
Reorganization of source code.
- bshow: Reorganized code to allow references between image and micrograph structures required for particle image extraction: 20040406
- Many files in the util directory was moved into img, mg,
mol and ps: 20040407
- bseries: Aligns a series of micrographs, update coordinates and extract particle images: 20040407
- Filter kernels added into the parameters directory: 20040416
- Better version control through the file BVERSION: 20040430
Version 1.1.1, 2004-08-23
A large amount of functionality was added to deal with user
requests. Final release from Caltech.
- read_star: Improved STAR file parsing speed: 20040517
- bimg: Deleting sub-images: 20040622
- bfilter: Denoising function and phases only filter: 20040703
- bradial: Averaged radial power spectrum: 20040707
- bcolour: Add single colour conversions: 20040708
- bpartsel: Added functions to set the FOM, select particles and set orientations based on the FOM of the first micrograph, and show particle parameters: 20040709
- bmg: Dump particle parameters into a table and change pixel size: 20040709
- bshow: Add dialog box for the power spectrum: 20040713
- btile, bpatch: Programs to fragment and reassemble images: 20040713
- bampweigh: Adjust the amplitudes of an image by those of a template: 20040714
- bar: Simple arithmetic on images: 20040727
- bpartmulti: Analyzing errors between two parameter files:
- bproject: Random projections: 20040731
- bop: Mask to limit region of comparison for fitting: 20040805
Version 1.2.0, 2004-11-04
Release from LSBR, NIAMS, NIH.
- CTF fitting: Major changes in the CTF fitting in bshow and bctf: 20041104
- borient: Major improvement in dealing with half asymmetric
Version 1.3.0, 2005-10-07
Release from LSBR, NIAMS, NIH.
- bflat: A solvent flattening program: 20041113
- dhand: Program to determine handedness from tilt pairs by
- Reorganized functionality of bpick and balign. New bpick
for finding and extracting particle images, new balign for aligning a
pair of micrographs, and bmgalign to align a large set of images
specified in a parameter file: 20041129
- bmultislice: Multi-slice single image simulation: 20041201
- bsim: Large-scale multi-slice image simulation: 20041201
- bphase: A program to examine and change phases: 20041208
- Added support for PNG (now requires zlib): 20041223
- Memory tracking improved (using the -v mem option): 20041225
- bcolour: Added CMYK support: 20050111
- bsplitmol: Program to split molecule groups into individual molecules: 20050119
- bresolve: Add an option to specify sampling of the resolution shells: 20050121
- bmoledit: Some coordinate editing functions: 20050122
- More functions distinguishing molecule groups from
individual molecules: 20050123
- bmd: Minimalistic implementation of molecular dynamics: 20050202
- bwater: Minimalistic molecular dynamics of blocks of water: 20050202
- bmolsym: Split out the symmetry functions from bmol: 20050214
- bshow: Added radial averaging for a powder diffraction
- Added support for the Wayne Hendrickson coordinate file format: 20050217
- bdif: Program to analyze diffraction patterns: 20050217
- balpha: Program to create and manipulate alpha helices:
- bfilter: Added a smoothing option for the bandpass filter:
- bmonte: Program to fit molecules into maps using monte carlo dynamics: 20050330
- Added 3D magnification for bshow: 20050405
- Introduced cross-validation for borient: 20050408
- Added use of BIOMT matrices in PDB files to bmolsym: 20050418
- Added use of SMTRY matrices in PDB files to bmolsym: 20050418
- Added linkers for markers in bshow: 20050514
- Added capability to pick multiple filaments in bshow: 20050612
- Introduced filament structures as part of the micrograph
- Changed support for PI from internal to M_PI from standard C: 20050704
- Changed the STAR structures to linked lists to remove limitations: 20050930
- Added support for Brookhaven STEM files: 20050811
- Expanded support for image with double precision data type:
- Numerous refinements of geometry functions with David Belnap: 20051005
Version 1.4.0, 2006-09-05
Release from LSBR, NIAMS, NIH featured in the paper: Heymann,
J. B. and Belnap, D. M. (2007). Bsoft: Image Processing and Molecular
Modeling for Electron Microscopy. J. Struct. Biol. 157(1), 3 - 18.
- bshow: Added a toolbar: 20051130
- Converted several structures to C++ classes: Complex, Vector3, Matrix3, Quaternion: 20051222
- btomo, btrack, btomrec, bmgft, bzfft, bmark: Programs for tomography: 20060122
- Converted Bstring to a C++ class: 20060127
- bshow: Added directional radial averages to the diffraction
- breconstruct: Modified to generate one map per filament: 20060304
- bmonte: Introduced adjustment of single atoms by Monte Carlo methods: 20060420
- bpick: Introduced capability to pick boxed particles along filaments: 20060425
- bmol: Added radial density function: 20060502
- bflood: Watershed segmentation algorithm (originally in bsegment): 20060511
- bsym: Added search for point group symmetry: 20060815
- bpartsel & breconstruct: Added bootstrap
- bshow: Added the selection tool functionality: 20060820
Version 1.5.0, 2007-10-25Release from LSBR, NIAMS, NIH associated with the paper: Heymann, J.B., Cardone, G., Winkler, D. and Steven, A.C. (2007) Computational resources for cryo-electron tomography in Bsoft. J. Struct. Biol. 161(3), 232 - 242.
- btomres: New program to estimate the resolution of aligned
tilt series: 20070216
- bfind: Added directional mode: 20070227
- bshow: Added refinement of tilt series parameters: 20070315
- bfind and bnorm: Added support for parameter files: 20070317
- bmedian: New program to do iterative median filtering:
- bbif: New program to do bilateral filtering: 20070404
- bmatrix: Added affinity propagation clustering: 20070419
- bsubvol: New program to select particles in a series: 20070419
- Extracted CTF parameters from Bimage into a new structure:
- bradial: Arbitrary radial step sizes in bradial: 20070514
- bmissing: New program to generate reciprocal space missing
region masks: 20070604
- bsymcomp: New program to fit symmetrized versions of molecules: 20070612
- bmodel: New program for managing low resolution models: 20070614
- Function to "untangle" molecules (bmoledit & bmodel): 20070614
- Model structures reorganized to allow multiple models and component definitions: 20070616
- Debugged bsplit to avoid core dumps and memory allocation errors: 20070814
- bmark: All vestiges of linkers removed, markers only from mg and rec: 20070903
- bshow: Introduced I/O code for model components and linkers: 20070903
- Model structures extended to include linkers and polygons: 20070903
- Chimera cmm marker format added: 20070905
- bmodmask: New program to generate masks from models: 20070905
- bpoly: New program to analyze and manipulate polyhedral models: 20070906
- bconvert: New program to convert lists of image files: 20070927
- MRC files: New specification switched to signed byte in stead of unsigned byte: 20070927
- dimgstats: New program to calculate Student's t-test: 20071004 (D.M.Belnap)
- bshow: Rearranged menus and introduce "Model" menu and model functions: 20071015
- bshow: Introduced code for helical diffraction processing: 20071015
Version 1.5.3, 2008-03-06Lots of new modeling code and bug fixes.
- Moved the CTF parameters out of the micrograph structure into a new structure: 20071110
- bpoly: Polyhedral symmetry determination: 20071125
- bpartsel: Sets generated can be contained within each micrograph: 20071127
- bpartmulti: Micrograph merging improved - can handle non-identical files: 20071127
- bpoly: Introduced angular restraints for regularization: 20071205
- Fixed jacobian rotation for eigen analysis: 20071206
- Added permutation generation: 20071206
- borient: Cross-validation is now calculated on excluded low resolution shells: 20071207
- bshow: Particle and filament image output can now be split to individual files: 20080203
- Path for extraction of particles fixed: 20080208
- Path for CTF corrected images fixed: 20080219
- bmask: New multi-level mask option: 20080225
- bass: New program to assemble molecules specified within models: 20080226
- blocres: New program to calculate local resolution: 20080229
Version 1.5.4, 2008-04-09Lots of new modeling code and bug fixes.
- bsym: Introduced replication of an asymmetric unit: 20080322
- View calculations modified for optimization and accuracy: 20080326
- bshow & bctf: Option to limit power spectrum generation along tilt axis: 20080328
- blocres: Introduced limiting calculation to an asymmetric unit: 20080328
- bradial: Fixed radial fitting to eliminate sporadic bad fits: 20080408
- Reorganized model I/O code: 20080408
- bspiral: New program to generate polyhedra: 20080408
- bdelta: New program to generate deltagraph polyhedra: 20080408
- bmodcol: New program to colour models: 20080408
Version 1.5.7, 2009-06-15New single particle analysis, helical processing and modeling code, introduction of XML and OpenMP support, as well as lots of bug fixes.
- bpartcen: New program to center single particle images: 20080425
- bmodcomp: New program to compare models to references: 20080428
- Updated the TIFF library to version 3.8.2: 20080523
- Multiple model format support improved: 20080604
- Improved support for 3D CTF for reconstructions: 20080705
- Added animation to bshow (Jeremy Greenfield): 20080725
- Improved object manipulation in bshow (Jeremy Greenfield): 20080725
- bxb: New program to extract and build densities: 20080728
- Change from STAR-specific tags to generic tags for parameter files: 20080924
- Added magnification field for sub-images: 20080930
- Introduced an XML format for micrographs: 20081028
- Introduced an XML format for models: 20081029
- First use of OpenMP capability in bnorm: 20081031
- Added support for the Princeton Instruments SPE format: 20081105
- bmodsel: New program to select model components: 20081114
- bmultifit: New program to search for multiple versions of a template in a map: 20081114
- brefine: New program to refine single particle orientations: 20081116
- bmodmap: New program to calculate a map from a model: 20081117
- bmod2part: New program to convert between model and particle coordinates: 20081117
- Added the extra programs directory: 20081119
- Added searching for helical parameters to bhelix: 20081206
- bmolhel: New program to generate a helix from an asymmetric unit: 20090121
- bfil: New program to extract filaments and derived particles (replaces some functions of bpick): 20090224
- bparam: New program to extract molecular modeling parameters from atomic coordinate files: 20090226
- Fixed SPIDER header for stack I/O: 20090423
Version 1.6.0, 2010-02-11Update to 3D single particle averaging and tomography, introduction of FFTW3 for use with OpenMP, several new programs for modeling, and lots of bug fixes.
- bfind: Update to fit into 3D averaging workflow: 20090709
- brecadd: New program to do 3D average: 20090709
- Added Xplor map format (.xpl): 20090713
- bshell: New program to generate spherical point models: 20090724
- bproject: Added OpenMP-based parallel projection generation: 20090806
- Added CTF consideration in borient, brefine and breconstruct: 20090810
- Added FFTW3 as alternative to FFTW (v2): 20090812
- Added OpenMP-based parallel Fourier transforms of multiple images: 20090812
- bradsec: New program to calculate symmetry-based radial sections: 20090823
- bzfft: Added ability to do z-line transforms on y tiles: 20090827
- brecmod: New program to link reconstructions and models: 20090922
- bshell: Added fitting, radial profile and power spectrum functions: 20090924
- bpatch: Added support for micrograph parameter files: 20090928
- bshow: Replaced object lists with direct calls to parameter structures: 20091009
- bmissing: Added generation of missing mask from tilt series orientations: 20091012
- Digital Micrograph format 3: Improved to read tags properly: 20091101
- baddmask: New program to combine masks into a composite mask: 20091117
- bmultimask: New program to manipulate composite masks: 20091209
- emgrand: New program for randomizing micrograph parameters: 20100128
- bmodedit: New program to create and edit models: 20100128
- dcount: New program to determine occupancies of proteins in tomograms: 20100205
- bdual: New program to aid in reconstructing dual tilt tomograms: 20100211
- bproject: Added reciprocal space projection: 20100211
Version 1.7.0, 2010-12-16Improved single particle analysis, tomographic 3D single particle analysis, and modeling with type specifications and selections.
- bshow: Better handling of component types and their properties through selection: 20100329
- bmm: New program to do model mechanics: 20100407
- borient: Projections now calculated by reciprocal space interpolation: 20100422
- CCP4 MAP and MRC: Added the STK type for 2D image stacks: 20100423
- MRC: Added support for IMOD-derived MRC format variants: 20100426
- b3v: New program to extract orthogonal views from a map: 20100429
- Cross-correlation normalization corrected: 20100616
- Added statistics to sub-image structure: 20100710
- Changed timer functions: 20100726
- IMAGIC images: Added ability to recognize old format: 20100802
- borient: Improved orientation finding in pps mode: 20100803
- borient: Improved orientation finding in ccc mode: 20100805
- View, Euler and Transform converted to class objects: 20100811
- brefine: Improved Monte Carlo refinements: 20100818
- Converted Bmatrix to a class object: 20100818
- brefine: Introduced grid search refinements: 20100819
- bshell: Added circle, ellipse and ellipsoid shapes: 20100827
- breconstruct: Introduced resolution estimate calculated during reconstruction: 20101018
- bhelix: Improved function to determine helical parameters: 20101102
- Changed to more rational kernel names in the parameter directory: 20101115
- bmg: Added option to use a different reference view (suggested by Eduardo Sanz-Garcia): 20101116
- emgrand: Added helical random views: 20101116
- bsym: Added option to change symmetry: 20101123
- bmodsel: Added FOM rank selection: 20101130
- bshow: Added voxel value recording feature: 20101202
- bbackproj: Improved R-weighting: 20101216