Wikibooks

Software Tools For Molecular Microscopy/Application tools

< Software Tools For Molecular Microscopy

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

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Leginon

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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.
  • Support: Operating systems: Linux/Windows Image format support: MRC
  • Cost: Free/Open source, Apache 2.0
  • Primary Publication to Cite:
    • Suloway C, Pulokas J, Fellmann D; et al. (2005). "Automated molecular microscopy: the new Leginon system". J. Struct. Biol. 151 (1): 41–60. doi:10.1016/j.jsb.2005.03.010. PMID 15890530. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  • Additional References:

SerialEM

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see Software_Tools_For_Molecular_Microscopy/Specific_packages#SerialEM

UCSF Tomography

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see Software_Tools_For_Molecular_Microscopy/Specific_packages#UCSF_Tomography

TOM Toolbox

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see Software_Tools_For_Molecular_Microscopy/Specific_packages#TOM_Toolbox

Particle Selection

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DoG Picker

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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

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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

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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. (2007). "SIGNATURE: A single-particle selection system for molecular electron microscopy". Journal of Structural Biology. 157: 168–173. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


SwarmPS

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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. (2007). "SwarmPS: Rapid, semi-automated single particle selection software". Journal of Structural Biology. 157: 174–188. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


TiltPicker

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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

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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. {{cite journal}}: Cite has empty unknown parameter: |month= (help)CS1 maint: multiple names: authors list (link)

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CTF Estimation and Correction

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ACE

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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. (2005). "ACE: Automated CTF Estimation". Ultramicroscopy. 104 (1): 8–29. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


ACE2

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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

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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. (2003). "Accurate determination of local defocus and specimen tilt in electron microscopy". Journal of Structural Biology. 142: 334–347. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


ctf Explorer

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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: , w:Postcardware, freeware
  • 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 (S02): 1572CD–1573CD. doi:10.1017.S1431927602104442. {{cite journal}}: Cite journal requires |journal= (help); Check |doi= value (help); Cite has empty unknown parameter: |pmcid= (help)


EMCTF

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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. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy. 106: 587–596. doi:10.1016/j.ultramic.2006.02.004. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Additional References:
    • Fernandez, J.J. (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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


TOMOCTF

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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. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy. 106: 587–596. doi:10.1016/j.ultramic.2006.02.004. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


fitctf

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Estimating contrast transfer function and associated parameters by constrained non-linear optimization
  • Support: Operating systems: Linux, Windows, and Mac OS X Image format support: MRC
  • Cost: free
  • Primary Publication to Cite:
    • Yang, C (2009). "Estimating contrast transfer function and associated parameters by constrained non-linear optimization". Journal of Microscopy. 233 (3): 391–403. doi:10.1111/j.1365-2818.2009.03137.x. PMID 19250460. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


FitCTF2

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A graph theory method for determination of cryo-EM image focuses
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Written In: Python
  • Primary Publication to Cite:
    • Jiang, Wen (2012). "A graph theory method for determination of cryo-EM image focuses". Journal of Structural Biology. 180 (2): 343–351. doi:10.1016/j.jsb.2012.07.005. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

3D Reconstruction

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TOMO3D

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


TOMO3Dhybrid

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

Resolution Estimation

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FSC

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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. (1986). "Exact filters for general geometry three dimensional reconstruction". Optik. 78: 146–156. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Additional References:
    • van Heel, M. (2005). "Fourier shell correlation threshold criteria". Journal of Structural Biology. 151: 250–262. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


RMEASURE

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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. (2007). "Ab initio resolution measurement for single particle structures". Journal of Structural Biology. 157: 201–210. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

Denoising

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iMed

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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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help)CS1 maint: multiple names: authors list (link)


TOMOAND

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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. (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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Additional References:
    • Fernandez, J.J. (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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)


TOMOBFLOW

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Package for noise reduction in electron tomography with Beltrami flow.


XMSF

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

Segmentation

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CoDiv

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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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help)


Population

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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:


TOMOSEGMEM

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Package for segmentation of membranes in tomograms.


TomoSegMemTV

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Package for robust membrane segmentation based on Tensor Voting for tomograms.

B-Factor Estimation and Correction

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bfactor

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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

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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. (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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Additional References:
    • Rosenthal, P.B. (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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

Initial Model Construction

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ROTAN

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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. (2008). "Angle determination for side views in single particle electron microscopy". Journal of Structural Biology. 162: 260–270. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Additional References:
    • Rubinstein, J.L. (2003). "Structure of the mitochondrial ATP synthase by electron cryomicroscopy". EMBO Journal. 22: 6182–6192. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
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