Software Tools For Molecular Microscopy/Application tools

Packages that offer a tool or a set of tools to permit the analysis of data in one or more class of structural problems. These have generally been developed to manage one specific step in the structural analysis, for example CTF correction, particle picking etc.

Data Acquisition

Leginon

Leginon is a system designed for automated collection of images from a transmission electron microscope. Instruments supported: FEI Tecnai series TEM, Tietz and Gatan CCD cameras. On August 1, 2007, Leginon 1.4 was released as open source.

SerialEM

see Software_Tools_For_Molecular_Microscopy/Specific_packages#SerialEM

UCSF Tomography

see Software_Tools_For_Molecular_Microscopy/Specific_packages#UCSF_Tomography

TOM Toolbox

see Software_Tools_For_Molecular_Microscopy/Specific_packages#TOM_Toolbox
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Particle Selection

DoG Picker

DoG Picker is a simple particle picker that picks particles that resemble a blob using the Difference of Gaussians algorithm. It is intergrated into the TiltPicker program (below),

FindEM

The FindEM program is based on projection matching using local real-space correlation with a series of templates. Real-space algorithms are traditionally relatively slow, but a fast Fourier based implementation of the real-space local correlation function has been introduced which is approximately two orders of magnitude faster for the projection matching application. This algorithm is referred to as the “Fast Local Correlation Function” or FLCF.
  • Support: Operating systems: Unix Image format support: MRC
  • Cost: Free/Open source
  • Primary Publication to Cite:
    • Roseman, A.M. (2004). "FindEM—a fast, efficient program for automatic selection of particles from electron micrographs". Journal of Structural Biology 145 (1-2): 91-99. doi:10.1016/j.jsb.2003.11.007. PMID 15065677. 
  • Additional References:
    • Roseman, A.M. (2003). "Particle finding in electron micrographs using a fast local correlation algorithm.". Ultramicroscopy 94 (3-4): 225–236. PMID 12524193. 

Signature

A particle selection system for molecular electron microscopy. It applies a hierarchical screening procedure to identify molecular particles in EM micrographs. The user interface of the program provides versatile functions to facilitate image data visualization, particle annotation and particle quality inspection. The system design emphasizes both functionality and usability.
  • Support: Operating systems: Linux, Mac OS X, MS Windows Image format support: MRC, TIFF
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Chen, J. Z.; Grigorieff, N. (2007). "SIGNATURE: A single-particle selection system for molecular electron microscopy". Journal of Structural Biology 157: 168-173. 

SwarmPS

A specialised graphical user interface designed to streamline the process of particle selection from electron micrograph data sets. It provides implementations of both template matching and edge detection algorithms, has an intuitive and easy to use interface, and can be used to obtain useful results on most data sets that are generated in electron microscopy. Currently users can expect to select about 1000-4000 particles per hour of interaction.
  • Support: Operating systems: Linux Image format support: Most image formats
  • Cost: Free for academic use under a software license agreement
  • Primary Publication to Cite:
    • Woolford, D.; Ericksson, G., Rothnagel, R., Muller, D., Landsberg, M. J., Pantelic, R. S., McDowall, A., Pailthorpe, B., Young, P. R., Hankamer, B., and Banks, J. (2007). "SwarmPS: Rapid, semi-automated single particle selection software". Journal of Structural Biology 157: 174-188. 

TiltPicker

A graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers.

TMaCS

Template Matching and Classification System. Template matching identifies candidate particle images while a Support Vector Machine algorithm is interactively trained to distinguish particles from non-particles.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free/Open Source
  • Primary Publication to Cite:
    • Zhao J, Brubaker MA, Rubinstein JL (2013). "TMaCS: A hybrid template matching and classification system for automated particle selection". J. Struct. Biol. In Press. 
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CTF Estimation and Correction

ACE

A completely automated algorithm for estimating the parameters of the contrast transfer function (CTF) of a transmission electron microscope. A MATLAB implementation of the algorithm, called ACE, is freely available. See also author's website: http://graphics.ucsd.edu/~spmallick/research/ace/index.html
  • Support: Operating systems: MATLAB Image format support: MRC
  • Cost: Free/Open Source, Apache License v2.0
  • Written In: MATLAB
  • Primary Publication to Cite:
    • Mallick, S.P.; B Carragher, CS Potter, DJ Kriegman (2005). "ACE: Automated CTF Estimation". Ultramicroscopy 104 (1): 8-29. 

ACE2

ACE2 is CTF estimation and correction program using the algorithms developed by Satya et al. (see ACE) rewritten in Objective-C programming language and does not require MATLAB.
  • Support: Operating systems: Unix (specifically, Mac OS X and Linux) Image format support: MRC
  • Cost: Free/Open source, Apache License v2.0
  • Written In: Objective-C
  • Primary Publication to Cite:
    • Unpublished

CTFfind3 and CTFtilt

Programs for finding CTFs of electron micrographs
  • Support: Operating systems: Linux, IRIX, OSF Image format support: MRC
  • Cost: Free/Open Source, GPL
  • Written In: Fortran
  • Primary Publication to Cite:
    • Mindell, J.A.; Grigorieff, N. (2003). "Accurate determination of local defocus and specimen tilt in electron microscopy". Journal of Structural Biology 142: 334-347. 

ctf Explorer

allows to calculate the Phase Contrast Transfer Function (CTF): a useful characteristics in Electron Microscopy
  • Support: Operating systems: Windows 95/98/NT4/2000/XP Image format support:
  • Cost:
  • Primary Publication to Cite:
    • Sidorov, Max V. (2002). ctfExplorer: Interactive Software for 1d and 2d Calculation and Visualization Of TEM Phase Contrast Transfer Function. 8. pp. 1572CD-1573CD. doi:10.1017.S1431927602104442. 

EMCTF

CTF determination of non-astigmatic images in electron cryomicroscopy
  • Support: Operating systems: Linux, Mac OS X Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Li, S. and Crowther, R. A. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy 106: 587-596. doi:10.1016/j.ultramic.2006.02.004. 
  • Additional References:
    • Fernandez, J.J.; Sanjurjo, J.R. and Carazo, J. M. (1997). "A spectral estimation approach to contrast transfer function detection in electron microscopy". Ultramicroscopy 68: 267-295. doi:10.1016/S0304-3991(97)00032-6. 

TOMOCTF

CTF determination and correction in electron tomography
  • Support: Operating systems: Linux, Mac OS X Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Li, S. and Crowther, R. A. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy 106: 587-596. doi:10.1016/j.ultramic.2006.02.004. 
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3D Reconstruction

TOMO3D

Fast tomographic reconstruction on standard multicore computers with WBP and SIRT.

TOMO3Dhybrid

Fast tomographic reconstruction (WBP,SIRT) with CPU+GPU co-processing
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Resolution Estimation

FSC

Program to calculate the Fourier Shell Correlation of two 3D volumes. The three-dimensional Fourier Shell Correlation (FSC) measures the normalised cross correlation coefficient between two 3D volumes over corresponding shells in Fourier space, i.e., as a function of spatial frequency. The (modified) 3-sigma criterion indicates where the FSC systematically emerges above the expected random correlations of the background noise. The 1/2-bit information threshold criteria express where we have already collected a sufficient amount of data in the final 3D reconstruction to allow a direct structural interpretation at that resolution level. The 1/2-bit curve is calibrated to approximately yield resolution values comparable to resolution values in use in X-ray crystallography (FOM).
  • Support: Operating systems: Linux/Unix, Mac OS X (Intel), MS Windows Image format support: IMAGIC, Spider, CCP4, MRC, TIFF, etc.
  • Cost: Free
  • Primary Publication to Cite:
    • Harauz, G.; M. van Heel (1986). "Exact filters for general geometry three dimensional reconstruction". Optik 78: 146–156. 
  • Additional References:
    • van Heel, M.; M. Schatz (2005). "Fourier shell correlation threshold criteria". Journal of Structural Biology 151: 250-262. 

RMEASURE

A computational method that allows the measurement of the signal-to-noise ratio and resolution of a three-dimensional structure obtained by single particle electron microscopy and reconstruction. The method does not rely on the availability of the original image data or the calculation of several structures from different parts of the data that are needed for the commonly used Fourier Shell Correlation criterion. Instead, the correlation between neighboring Fourier pixels is calculated and used to distinguish signal from noise.
  • Support: Operating systems: Linux, IRIX, OSF, Mac OS X Image format support: MRC, Spider
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Sousa, D.; N. Grigorieff (2007). "Ab initio resolution measurement for single particle structures". Journal of Structural Biology 157: 201-210. 
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Denoising

iMed

Software for automatic noise reduction using iterative median filtering.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • van der Heide P, Xu XP, Marsh BJ, Hanein D, Volkmann N (2007). "Efficient automatic noise reduction of electron tomographic reconstructions based on iterative median filtering". J. Struct. Biol. 158: 196-204. PMID 17224280. 

TOMOAND

Package for noise reduction in electron cryotomography with Anisotropic Nonlinear Diffusion.
  • Support: Operating systems: Linux, Mac OS X Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Li, S. (2003). "An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms". Journal of Structural Biology 144: 152-161. doi:10.1016/j.jsb.2003.09.010. 
  • Additional References:
    • Fernandez, J.J.; Li, S. and Lucic, V. (2007). "Three-dimensional anisotropic noise reduction with automated parameter tuning. Application to electron cryotomography". Lecture Notes in Computer Science 4788: 60-69. doi:10.1007/978-3-540-75271-4_7. 

TOMOBFLOW

Package for noise reduction in electron tomography with Beltrami flow.

XMSF

Package for noise reduction and pre-segmentation in electron tomography based on Mean-Shift.
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Segmentation

CoDiv

CoDiv - Continental Divide Watershed Segmentation. Software for semi-automatic segmentation of density maps such as those obtained by electron microscopy and image reconstruction or electron tomography.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Volkmann N (2002). "A novel three-dimensional variant of the watershed transform for segmentation of electron density maps". J. Struct. Biol. 138: 123-129. PMID 12160708. 

TOMOSEGMEM

Package for segmentation of membranes in tomograms.

Population

CoDiv - Population is dedicated to the quantitative/qualitative analysis of images coming from 2D/3D microscopy with filtering, segmentation, geometrical/physical characterization, visualization and modeling.
  • Support: Operating systems: Linux/Windows Image format support: RAW/BMP/JPEG/PNG/PGM
  • Cost: Free for academic/industrial users, MIT
  • Written In: C++
  • Primary Publication to Cite:
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B-Factor Estimation and Correction

bfactor

Program for filtering 3D maps and applying B-factors.
  • Support: Operating systems: Linux/Mac Image format support: MRC
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Unpublished

EM-BFACTOR

Package for sharpening high resolution information in single particle electron cryomicroscopy
  • Support: Operating systems: Linux, Mac OS X Image format support: Most common formats used in 3DEM
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Luque, D., Caston, J.R., Carrascosa, J.L. (2008). "Sharpening high resolution information in single particle electron cryomicroscopy". Journal of Structural Biology 164: 170-175. doi:10.1016/j.jsb.2008.05.010. 
  • Additional References:
    • Rosenthal, P.B.; Henderson, R. (2003). "Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy". Journal of Molecular Biology 333: 721-745. doi:10.1016/j.jmb.2003.07.013. 
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Initial Model Construction

ROTAN

Program for estimating the relative angular orientation of single particles that present side views
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Baker, L.A.; Rubinstein, R. (2008). "Angle determination for side views in single particle electron microscopy". Journal of Structural Biology 162: 260-270. 
  • Additional References:
    • Rubinstein, J.L.; Walker, J.E. and Henderson, R. (2003). "Structure of the mitochondrial ATP synthase by electron cryomicroscopy". EMBO Journal 22: 6182-6192. 
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Last modified on 17 May 2013, at 17:30