# 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