Table 8.1
Software packages with tools for tomographic reconstruction (For more, see https://en.wikibooks.org/wiki/Software_Tools_For_Molecular_
Microscopy)
Package
Algorithm(s)
Remarks
Coding environment
Web site
References
ASTRA toolbox
WBP, SIRT, CGLS
Flexible plugins
CUDA/C++/
Matlab/python
http://visielab.uantwerpen.be/research/tomography
[87]
ATOM/ICON/FIRT
WBP, ART, SIRT, FIRT, ICON
C
http://feilab.ibp.ac.cn/LBEMSB
[67, 88, 89]
Bsoft
FSR
Simultaneous dual tilt reconstruction
C++/TclTk
http://bsoft.ws
[12]
EM3D
WBP
Defunct? (last 2011)
Java/C++
–
http://em3d.stanford.edu
[90]
Ettention
WBP, BIR, TF-ART, SIRT, SART
Integrated into eTomo
C++/Java
http://www.ettention.org
[91]
IMOD/
eTomo
WBP, GFSR, SIRT
Combining dual tilt and large volume tomograms
FORTRAN/C/Java
http://bio3d.colorado.edu/imod/
[27]
Protomo
WBP
FORTRAN/C/Python
http://www.electrontomography.org
[92]
PyTom
WBP, INFR
C++/Python
http://pytom.org
[73]
Tom toolbox
WBP
Matlab
http://www.biochem.mpg.de/tom/
[93]
Tomo3D
WBP, SIRT
C (threaded)
https://sites.google.com/site/3demimageprocessing/tomo3d
[94]
TomoJ
WBP, ART, SIRT
ImageJ plugin
Java
http://cmib.curie.fr/en/download/softwares/TomoJ
[95]
TxBR
WBP
Large volume reconstruction
Matlab
https://confluence.crbs.ucsd.edu/display/ncmir/TxBR
[96]
Xplore3D (FEI)
WBP, ART, SIRT
Proprietary
(Windows)
http://www.fei.com/life-sciences/
WBP
Weighted back-projection
FSR
Frequency space reconstruction
GFSR
Gridded frequency space reconstruction
INFR
Iterative non-uniform fast Fourier reconstruction
ART
Algebraic reconstruction technique
TF-ART
Tilt-focal ART
ATOM
Algebra TOMography package
FIRT
Filtered iterative reconstruction technique
ICON
Iterative compressed-sensing optimized non-uniform fast Fourier transform reconstruction
SIRT
Simultaneous iterative reconstruction technique
SART
Simultaneous algebraic reconstruction technique
BIR
Block-iterative reconstruction
CGLS
Krylov subspace least squares congruent gradients analytical solver
212
J. Bernard Heymann