Change History of Bsoft Version 2, 2017-2019
Version 2.0.0, 20171117
First release of the transition to a modern version of Bsoft
- Reorganized the compilation to use the make utility: 20171117
- Incorporated the Radon package: 20171117
Version 2.0.2, 20180703
Introducing new C++ concepts into Bsoft
- A JSON parser and management: 20180409
- bico: Program to analyze icosahedral particles: 20180503
- breconstruct: Added resolution estimation from halfmaps: 20180524
Version 2.0.3, 20180905
Adding more functionality to Bsoft
- bnad: Switched to Kopp 3x3 eigen analysis: 20180723
- bmissing: Added option to find missing regions in a map and create a mask: 20180914
Version 2.0.5, 20190711
Adding more functionality to Bsoft
- btomo: Thickness estimation from intensity changes: 20181227
- Added reading of SerialEM mdoc files: 20190109
- btomaln: Fiducialless tilt series alignment: 20190131
- btomaln: Includes thickness estimation: 20190131
- bctf: Improved tilted power spectrum generation: 20190210
- bsupix: Added option to various feature asignments: 20190314
- bstar: Added option to examine the header: 20190410
- bsym: Added option to rotate to a desired axis: 20190417
- beditimg: Added Gaussian sphere: 20190506
- bmaxpow: Parallelized and improved: 20190516
- bsf: Added option for correct scaling based on acceleration voltage: 20190702
Version 2.0.6, 20191126
Adding more functionality to Bsoft
- bshow: Added workflow for SPA: 20190715
- bmatch: A new program to search for projections from a 3D map in a 2D image: 20190821
- borient: Default cross-validation is now calculated for 10% beyond the high resolution limit (same as brefine): 20190821
- MRC: Added IMOD unsigned/signed byte switch: 20190827
- bseries: Modified output option - now "-write sum": 20190917
- Separate pixel size for particles: 20191015
- Extract particles at sampling different from micrograph: 20191015
- bshow: Added a file browser: 20191105
Version 2.0.7, 20191230
Adding more functionality to Bsoft
- bseries: Added frame rate option: 20191120
- bseries and bampweigh: Modified -dose option to accept dose/frame: 20191125
Version 2.1.0, 20201023
Adding more functionality to Bsoft
- bctf: Added JSON file I/O: 20200525
- bsegment: Added K-means segmentation: 20200527
- bhead: Added flag for different backgrounds: 20200610
- bflood: Reorganized options: 20200611
- btomres: Added NLOO3D calculation: 20200723
- bmultimask: Incoroporated blevel functionality: 20200821
- bproject: Added matrix output option: 20201016
- bmodcomp: Added matrix output option: 20201017
- bmol: Added matrix output option: 20201017
- bseqaln: Added matrix output option: 20201017
- bcormut: Added matrix output option: 20201017
- bcormut: Added reference sequence option: 20201017
Version 2.1.1, 20210228
Adding more functionality to Bsoft
- bfilter: Added frequency and Gabor filters: 20210127
- bshow: Added Gaussian fits to histogram: 20210202
- bstar: Started introducing new STAR access code: 20210214
- bscatter: New program to calculate electron scattering parameters: 20210215
- Models: Large-scale change in modeling objects: 20210220
- bgradient: New program to calculate image gradients: 20210223
- GRD format: Extended data types and implemented run-length encoding: 20210223
- bshow: Added a scale bar: 20210226
- bgradient: Added kernel-based gradient calculation: 20210228
- bmultimask: Added conditional mult-level mask: 20210228
- bfft: Added FFT of multi-channel images: 20210228
- GRD format: Full set of Bsoft data types: 20210304
Version 2.1.2, 20210720
Adding more functionality to Bsoft
- star.h: Final conversion to new STAR access code: 20210330
- bpartsel: Add option to export particle list: 20210412
- bimport: New program to set up SPA from images: 20210413
- bseries: Added SSNR for frames: 20210614
- bpartsel: Improved filament direction assessment: 20210517
- beditimg: Added chirp image: 20210518
- EER format: Added TIFF EER codec: 20210615
- bseries: Added moving frame sum for alignment: 20210621
- EER format: Incorporated EER library support: 20210624
- ND2 format: Added: 20210628
- bmg: Added plot of micrograph origins: 20210706
- btomaln: Improved alignment to sub-images: 20210715
- btomrec: Reduced some excluded volume artifacts: 20210716
Version 2.1.3, 20210901
Adding more functionality to Bsoft
- bseries: Added subset and progressive SSNR: 20210805
- bseries: Improved frame alignment from subsets: 20210805
- bhisto: Added new counts detection from histogram: 20210805
- bmodel: Added link generation between specific types: 20210828
- bseries: Fit noise curves after SSNR calculation: 20210830
Version 2.1.4, current
Adding more functionality to Bsoft
- rwmgRELION.cpp: Updated for Relion 3.1: 20211224
- PDB: Added reading PDB files as models: 20220101
- CIF: Added reading CIF files as models: 20220101
- bproject: Added Ewald sphere projection: 20220104
- breconstruct: Added Ewald sphere reconstruction: 20220104
- blocres: Fixed an error in symmetry replication: 20220104
- blocres: Rearranged threading to speed up calculations: 20220104
- bpart: Added particle reference correlation sum: 20220104
- rwmgRELION.cpp: Added reading of Zernike coefficients: 20220105
- Aberrations: Added abberation parameters to ctf.h: 20220105
- baberr: New program to calculate aberration images: 20220105
- bpart: Added phase difference calculation: 20220124
- Aberrations: Converted all CTF parameters to a unified aberration scheme: 20220315
- bdif: Added option to find reflections at a given frequency: 20220318
- bess: New program for electron scattering simulation: 20220325
- XYZ: Added Kirklands XYZ format for atomic models: 20220426
- TrigLUT: Added trigonometric look-up tables: 20220717
- Options: Specifying units (such as "k" for 1000s): 20220722
- FFT: Introduced spcifications for backtransform: complex, real, imaginary, amplitudes or intensities: 20220808
- borient: Added option to invert reference contrast: 20220906
- bmodsym: Added lattice (crystal) generation: 20230118
- bcrystal: Reworked to use general models: 20230120
- bfocal: New program for analysing focal series micrographs: 20230128