Change History of Bsoft Version 1, 1999-2017

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

Release from LSBR, NIAMS, NIH.

bflat: A solvent flattening program: 20041113
dhand: Program to determine handedness from tilt pairs by David Belnap: 20041117
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 pattern: 20050216
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: 20050323
bfilter: Added a smoothing option for the bandpass filter: 20050328
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 database: 20050616
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: 20051004
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 plot: 20060201
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 reconstruction: 20060819
bshow: Added the selection tool functionality: 20060820

Version 1.5.0, 2007-10-25

Release 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: 20070329
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: 20070504
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, 2008-03-06

Lots 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, 2008-04-09

Lots 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, 2009-06-15

New 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, 2010-02-11

Update 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, 2010-12-16

Improved 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

Version 1.8.0, 20120229

Comprehensive change to C++ image objects, updated included libraries and new functions.

PNM: Added support for PBM, PGM and PPM image formats: 20110317
libtiff: Updated to version 3.9.4: 20110320
libpng: Updated to version 1.5.1: 20110320
zlib: Updated to version 1.2.5: 20110320
bgraphseg: New program to do graph-based segmentation: 20110328
Introduced the enumerated CompoundType: 20110618
Converted Complex to a two-channel compound type: 20110618
Converted Bimage and Bsub_image to classes: 20110810
bcyl: A new program for cylindrical operations: 20110930
bnad: Rewrote code to allow for threading: 20111003
Color classes RGB, RGBA, CMYK: 20111123
CTFparam class: 20111123
Reorganized cross-correlation functions to allow both resolution limits and mask: 20111128
bhelix: Symmetrization with a seam: 20120112
Bplot and associated classes: 20120118
Constant RHO changed to 0.81 Da/A3: 20120123

Version 1.9.0, 20150213

Further conversion to C++ syntax, threading and addition of new programs.

borient and brefine: Added mask option: 20120412
btompart: New program to reconstruct tomographic particles and estimate resolution: 20120416
Fixed cross-correlation roundoff error: 20120501
borient: Added polarresolution option: 20120506
Fixed issues with VMS with Jouk Jansen's help: 20120517
blocres: Parallelized: 20120731
blocfilt: Filter a map based on local resolution by Giovanni Cardone: 20120803
breconstruct: Introduced threading and modifying options: 20120913
Tcl/Tk code: Separated micrograph elements into different files: 20120926
dhand: Fixed and updated for proper output: 20121013
bmultifit: Modification to accumulate hits on a view grid: 20121013
bresolve: Added mask input option: 20121101
bhelix: Fixed helix parameter search -> findcc and findrs: 20121108
DM4: Support for Digital Micrograph format 4 images: 20121108
dhand: Improved handling of handedness analysis: 20121116
bresolve: XML output of a FSC curve improved: 20121217
bampweigh: Introduces option to read a FSC curve: 20121217
rwPDB: Fixed secondary structure parsing and writing: 20130111
bflood: Watershed algorithm threaded: 20130122
brun: Reorganized parsing and presentation: 20130123
brefine: Downsized reference map based on resolution limit: 20130201
EMX: Introduced micrograph exchange format support: 20130201
brefine: Introduced 1D weight function, default C-curve: 20130410
bfcc: New program to do fast cross-correlation searches: 20130618
Threaded background calculation code: 20130625
Bshow: Added "Change image" option to micrograph menu: 20130726
Changed from box radius to box size for particles: 20130805
Bshow: Added window and autoscaling preferences: 20130828
borient and brefine: Added ppx files to track particle alignment completion: 20130828
btomrec: Threaded micrograph transformation and pack in smaller reciprocal space: 20130829
btube: New program to symmetrize hexagonal tubes: 20131023
bhelix: Threaded helical symmetrization: 20131028
bhelcross: New program to reconstruct a cross section based on helical parameters: 20131028
bfilwidth: New program to estimate filament width: 20131028
Introduce Grand Central Dispatch as alternative to OpenMP: 20131211
Bshow: Filament profiles: 20131216
bpick: New algorithm based on circular foreground-background comparisons: 20140108
bhelix: Helical segment cross-correlations over an angular range: 20140207
bpath: New program to analyze paths in models: 20140325
Bshow and bfil: Added an automated filament node centering function: 20140411
bresolve: Add option to indicate high resolution limit used in alignment: 20140416
bspr: New program to do single particle reconstructions: 20140418
bxml: New program to read, write and validate XML files: 20140423
bdens: New program to calculate regional density averages: 20140424
bproject: -compare option with optional SNR imposed: 20140506
bpartsel: -filament option sets directional selection: 20140508
Digital Micrograph format: Rewritten with plist output: 20140516
bmgtransfer: New program to copy sets of parameters between parameter files: 20140403
bbild: New program to convert models to Bild representations for Chimera: 20140406
bshow: Added micrograph change buttons to boxing and CTF dialogs: 20140411
bctf: Added envelope equation choices: 20140710
borient: Reorganized orientation-finding code: 20140710
bseries: Threaded alignment: 20140710
bhelcross: Added an alignment option: 20140710
bplane: New program to manipulate plane models: 20140929
Jsubtomo: Incorporated and paralellized jsubtomo: 20150108
Added support for the FEI SER image format: 20150204

Version 1.9.3, 20161031

Bug fixes, modifications and additions.

Situs: Added support for the Situs image format: 20150316
OpenDX: Added support for the DX image format: 20150319
bbackproj: Fixed the weighting: 20150814
TGA: Added support for the TrueVision image format: 20150815
bpick and bshow: Templated particle picking: 20160106
Tilted CTF: Power spectrum and correcting for micrographs of tilted specimens: 20160123
Frames: Added frames tag to micrograph data block: 20160309
bseries: Progressive and iterative micrograph frame alignment: 20160309
bshell: New option to generate a shell model from each component: 20160531
bmodsym: New program for symmetry functions, including cyclic symmetry at components: 20160606
FOM block: Eliminated image FOM block - replaced by linked image(s): 20160606
bpick: New option to pick symmetry related subvolumes: 20160610
Bimage: Coverted the vast majority of image processing into the Bimage class: 20160616
bnad: Added support 2D images: 20160623
bctf: Added extra baselines to model peak at ~3.8 Å: 20160909
bmodcomp: Added model comparisons and consolidation: 20161012
Radon package: Updated: 20161025

Version 1.9.4, 20170426

Bug fixes, modifications and additions.

blevel: New program to handle level masks: 20161205
bftr: New program to resize images in frequency space: 20161205
bhead: Added moments calculation: 20161205
bfilter: Added difference-of-gaussians filter: 20161214
bscale: New program to rescale maps with minimal interpolation: 20170126
bsupix: New program to do superpixel segmentation: 20170421

Version 1.9.5, 20170918

Final version before big transition to version 2.

bmg2imod: Program to convert IMOD parameter files: 20170918
bmgconvert: Program to convert parameter files from other packages: 20170918
bmaxpow: New program to determine particle orientations from maximum power in transforms: 20171113