Version 0.1, 1999-11-30

Final 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, 2000-03-30

Final release of development at the Biozentrum, Basel.

Ported to VMS: 20000112
FFTW and LIBTIFF included in the distribution: 20000303

Version 0.3, 2000-11-01

Development 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, 2000-12-12

Release 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, 2001-05-27

Released at the Gordon conference on 3D electron microscopy in Rhode Island.

bctf: Determines and applies CTF.

Version 0.7, 2001-11-05

Production 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, 2002-05-27

Production version update.

breconstruct: Fourier space reconstruction from 2D images.
bsegment: Segments images in various ways.

Version 0.9, 2002-12-20

Production 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, 2003-11-28

Pre-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: 20030512
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 the 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: 20031102

Version 1.0.0, 2004-01-15

First 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 bcc: 20040401
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: 20040728
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 units: 20041104

Version 1.3.0, 2005-10-07