Project

General

Profile

Edit History

Software » History » Version 6

Sargis Dallakyan, 04/08/2015 06:24 PM

1 1 Sargis Dallakyan 
h1. Software
2 





    3
    
    
    
* [[ACE]] Automated CTF Estimation





    4
    
    
    





    5
    
    
    
* [[ACE2]] A CTF Estimator (ACE) 2. ACE2 is a completely rewritten version of ACE. ACE2 adds the additional feature of robust astigmatism estimation and CTF correction with astigmatism using either a mild Weiner filter (recommended) or phase-flipping. Since ACE2 in written in objective C, it no longer requires MATLAB to work.





    6
    
    
    





    7
    
    
    
* "Appion":http://emg.nysbc.org/projects/appion/wiki Appion is a "pipeline" for single particle reconstruction integrated with Leginon data acquisition. It consists of a web based user interface linked to a set of python scripts that control several underlying processing packages. These include EMAN, Spider, findem, ACE, Chimera, and more. All data input and output is managed by the database. The ultimate goal is to have all control of the processing pipeline managed from the web based user interface and all output from the processing presented using web based viewing tools. These notes are provided as a rough guide to using the pipeline but are not guaranteed to be up to date or accurate.





    8
    
    
    





    9
    
    
    





    10
    
    
    
* [[DoGpicker]] Particle picker that uses difference of Gaussians (DoG) for picking particles





    11
    
    
    





    12
    
    
    
* [[FindEM]]  Fast local correlation function particle picker





    13
    
    
    





    14
    5
    Sargis Dallakyan
    
* "Leginon":http://emg.nysbc.org/projects/leginon/wiki 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.





    15
    1
    Sargis Dallakyan
    





    16
    
    
    
* [[OptiMod]] A general, automated procedure for reconstructing and optimizing 3D models using common-lines methodologies.





    17
    
    
    





    18
    
    
    
* [[pyScope]] A Python extension for controlling Transmission Electron Microscopes and CCD cameras.





    19
    
    
    





    20
    
    
    
* [[TiltPicker]] A specially designed particle picker for image tilt pairs.





    21
    
    
    





    22
    
    
    
* [[Viewit]] A multidimensional image processing package.





    23
    
    
    





    24
    
    
    
* [[XMRBS-Scheduler]] A web based facilities scheduler





    25
    
    
    





    26
    
    
    
* [[Protomo 2.0]] Tomography - Tilt Series Aligner