SBGrid Consortium - Supported Software

Tomography

SBGrid supports 5 tomography software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title	Description	Linux 32-bit	Linux 64-bit	OS X Intel	Links	HiddenDetail
Electra	- (ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes ...	check	check	check		(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography. Developers Giovanni Cardone Categories Tomography Versions Linux 32: 0.5.2 Linux 64: 0.5.2 OSX Intel: 0.5.2 OSX PPC: 0.5.2 Citations Cardone et al. A resolution criterion for electron tomography based on cross-validation. Journal of structural biology (2005) vol. 151 (2) pp. 117-29 Technical Notes The website for this application is no longer available. License Type This software is distributed under an Open license.
(ELECtron Tomography Resolution Assessment) a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography. Developers Giovanni Cardone Categories Tomography Versions Linux 32: 0.5.2 Linux 64: 0.5.2 OSX Intel: 0.5.2 OSX PPC: 0.5.2 Citations Cardone et al. A resolution criterion for electron tomography based on cross-validation. Journal of structural biology (2005) vol. 151 (2) pp. 117-29 Technical Notes The website for this application is no longer available. License Type This software is distributed under an Open license. Static link to the SBGrid Electra page.
EMAN2	- a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 ...	check	check	check		a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library. The new system offers an easily extensible infrastructure, better documentation, easier customization, etc. However, it will be some time before the full capabilities of EMAN1 have been reimplemented in the new system. For this reason EMAN2 was designed to happily coexist with EMAN1 installations. It is strongly recommended that all EMAN2 installations be accompanied by an EMAN1 installation. The programs that DO exist in EMAN2 will generally be more capable and efficient than the EMAN1 counterparts. Developers Steven Ludtke Categories Electron Microscopy Tomography Versions Linux 32: 2.04 Linux 64: 2.04 OSX Intel: 2.04 OSX PPC: 20090618 Citations Tang et al. EMAN2: an extensible image processing suite for electron microscopy. Journal of structural biology (2007) vol. 157 (1) pp. 38-46 License Type This software is distributed under an Open license.
a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library. The new system offers an easily extensible infrastructure, better documentation, easier customization, etc. However, it will be some time before the full capabilities of EMAN1 have been reimplemented in the new system. For this reason EMAN2 was designed to happily coexist with EMAN1 installations. It is strongly recommended that all EMAN2 installations be accompanied by an EMAN1 installation. The programs that DO exist in EMAN2 will generally be more capable and efficient than the EMAN1 counterparts. Developers Steven Ludtke Categories Electron Microscopy Tomography Versions Linux 32: 2.04 Linux 64: 2.04 OSX Intel: 2.04 OSX PPC: 20090618 Citations Tang et al. EMAN2: an extensible image processing suite for electron microscopy. Journal of structural biology (2007) vol. 157 (1) pp. 38-46 License Type This software is distributed under an Open license. Static link to the SBGrid EMAN2 page.
IMOD	- a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction ...	check	check	check		a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial- and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and displaying the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong at the Boulder Laboratory for 3-D Electron Microscopy of Cells. Developers David Mastronarde Categories Electron Microscopy Tomography Versions Linux 32: 4.5.2 Linux 64: 4.5.2 OSX Intel: 4.5.2 OSX PPC: 4.1.9 Citations Kremer et al. Computer visualization of three-dimensional image data using IMOD. J Struct Biol (1996) vol. 116 (1) pp. 71-6 Mastronarde. Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol (1997) vol. 120 (3) pp. 343-52 License Type This software is distributed under an Open license.
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial- and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and displaying the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong at the Boulder Laboratory for 3-D Electron Microscopy of Cells. Developers David Mastronarde Categories Electron Microscopy Tomography Versions Linux 32: 4.5.2 Linux 64: 4.5.2 OSX Intel: 4.5.2 OSX PPC: 4.1.9 Citations Kremer et al. Computer visualization of three-dimensional image data using IMOD. J Struct Biol (1996) vol. 116 (1) pp. 71-6 Mastronarde. Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol (1997) vol. 120 (3) pp. 343-52 License Type This software is distributed under an Open license. Static link to the SBGrid IMOD page.
Priism/IVE	- the graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with ...	check	check	check		the graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism. Developers IVE Developer Group Categories Electron Microscopy Tomography Versions Linux 32: 4.2.7 Linux 64: 4.2.7 OSX Intel: 4.2.7 OSX PPC: 4.2.7 Citations Chen et al. IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications. Journal of structural biology (1996) vol. 116 (1) pp. 56-60 Chen, H., Clyborne, W., Sedat, J.W., and Agard, D. A. (1992) PRIISM: an integrated system for display and analysis of three-dimensional microscope images. Proceedings of SPIE - the International Society for Optical Engineering. 1660: 784-790. License Type This software is distributed under an Open license.
the graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism. Developers IVE Developer Group Categories Electron Microscopy Tomography Versions Linux 32: 4.2.7 Linux 64: 4.2.7 OSX Intel: 4.2.7 OSX PPC: 4.2.7 Citations Chen et al. IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications. Journal of structural biology (1996) vol. 116 (1) pp. 56-60 Chen, H., Clyborne, W., Sedat, J.W., and Agard, D. A. (1992) PRIISM: an integrated system for display and analysis of three-dimensional microscope images. Proceedings of SPIE - the International Society for Optical Engineering. 1660: 784-790. License Type This software is distributed under an Open license. Static link to the SBGrid Priism/IVE page.
Protomo	- includes programs and shell scripts for electron tomography of thin specimens. Protomo provides an interactive graphical tool ...	check	check			includes programs and shell scripts for electron tomography of thin specimens. Protomo provides an interactive graphical tool for a fast initial alignment of a tilt series and shell scripts for the more time consuming refinement, as well as some other useful image manipulation utilities. The package was originally developed for the reconstruction of thin sections of insect flight muscle. More recently, it has also been successfully applied in cryo-electron tomography. Developers Hanspeter Winkler Categories Tomography Versions Linux 32: 1.1.4 Linux 64: 1.1.4 Citations Taylor et al. The use of electron tomography for structural analysis of disordered protein arrays. Journal of structural biology (1997) vol. 120 (3) pp. 372-86 Winkler and Taylor. Focus gradient correction applied to tilt series image data used in electron tomography. Journal of structural biology (2003) vol. 143 (1) pp. 24-32 Winkler and Taylor. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy (2006) vol. 106 (3) pp. 240-54 License Type This software is distributed under an Open license.
includes programs and shell scripts for electron tomography of thin specimens. Protomo provides an interactive graphical tool for a fast initial alignment of a tilt series and shell scripts for the more time consuming refinement, as well as some other useful image manipulation utilities. The package was originally developed for the reconstruction of thin sections of insect flight muscle. More recently, it has also been successfully applied in cryo-electron tomography. Developers Hanspeter Winkler Categories Tomography Versions Linux 32: 1.1.4 Linux 64: 1.1.4 Citations Taylor et al. The use of electron tomography for structural analysis of disordered protein arrays. Journal of structural biology (1997) vol. 120 (3) pp. 372-86 Winkler and Taylor. Focus gradient correction applied to tilt series image data used in electron tomography. Journal of structural biology (2003) vol. 143 (1) pp. 24-32 Winkler and Taylor. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy (2006) vol. 106 (3) pp. 240-54 License Type This software is distributed under an Open license. Static link to the SBGrid Protomo page.