Some useful links in 3DEM

Single particles reconstruction:

Eman Home Page
Software for Single Particle Analysis and Electron Micrograph Analysis developed by Steve Ludtke at the National Center for Macromolecular Imaging at Baylor College.

Spider Manual of Operations
SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy, developed by Joachim Frank at the Wadsworth Center (New York State Department of Health, Albany).

Virus Reconstruction:

Auto3dem documentation
AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles developed by Tim Baker at UCSD.

Tomography Reconstruction:

Imod Home Page
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. 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.

CTF correction:

ACE Documentation
ACE is a MATLAB Toolbox for automatically recovering the parameters of the contrast transfer function ( including astigmatism ), the envelope function and the noise noise spectrum from images of carbon or particles embedded in ice. The algorithm was jointly developed by Satya P. Mallick , David Kriegman, Clint Potter and Bridget Carragher.

Data Collection :

Serial EM Home Page
SerialEM is a program to acquire tilt series for electron tomography on Tecnai and JEOL microscopes. SerialEM was developed primarily by David Mastronarde at the Boulder Laboratory for 3-D Electron Microscopy of Cells.

Leginon Home Page
Leginon is a system designed for automated collection of images from a transmission electron microscope. Leginon was developed primarily by Bridget Carragher and Clint Potter at AMI, The Scripps Research Institute.

Molecular Docking:

Situs Home Page
Situs is a package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. It has been developed mainly by Willy Wriggers at Biomachina.

CoAn
A package for docking atomic resolution structure into EM density. CoAn has been developed mainly by Niles Volkmann at the Burnham Institute for Medical Research.

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