Computational Methods for 3DEM
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Software
Contents
1
Electron Tomography
2
Single particle electron microscopy
3
Scientific computing
Other packages for 3DEM
developed by the EM community:
Software tools for molecular microscopy
Electron Tomography
CTF Determination and Correction
TOMOCTF
Package for CTF determination and correction in electron cryotomography
Tomographic Reconstruction
TOMO3D
Package for fast tomographic reconstruction on standard multicore computers
TOMO3DGPU
Package for tomographic reconstruction with matrix weighted backprojection on GPUs
TOMOEGEE
A user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography
Denoising
TOMOAND
Package for noise reduction in electron cryotomography
TOMOBFLOW
Package for feature-preserving noise filtering in electron tomography
TOMOXSMF
Package for feature-preserving noise filtering based on Mean-Shift filter
Single particle electron microscopy
CTF Determination
EMCTF
Package for CTF determination of non-astigmatic images in electron cryomicroscopy
3D Reconstruction
Xmipp
Our parallel programs for 3D reconstruction in single particle electron microscopy have been integrated into Xmipp:
mpi_reconstruct_art
,
mpi_reconstruct_wbp
,
reconstruct_art
B-factor estimation and correction
EMBFACTOR
Package for sharpening high resolution information in single particle electron cryomicroscopy
Creation of phantoms
Phan3D
Program for design of biological phantoms in 3D electron microscopy
Scientific computing
spmvELLRT
A library for efficient sparse matrix vector product on GPUs