ACE: Automated CTF Estimation


ACE

About
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. It requires the MATLAB image processing and optimization toolboxes.  The algorithm was jointly developed by Satya P. Mallick , David Kriegman, Clint Potter and Bridget Carragher.  The core code is written and maintained by  Satya P. Mallick. The code for integration with Leginon database is written by Denis Fellman.  For questions and comments,  mail to spmallick@graphics.ucsd.edu.

License
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free SoftwarFoundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

Distribution
ACE is distributed as a tarball (ace_version.tgz ) which is available in the following at the following locations
http://ami.scripps.edu/software/ace/
http://graphics.ucsd.edu/~spmallick/research/ace/
The later link contains all previous versions.

Installation

System Requirement: ACE is tested on MATLAB 7.00 and 7.01.  running on Linux. Although not tested extensively for any other *nix OS , Windows or MAC, it should work.  A machine with 1GB RAM is recommended for processing images of size 4k x 4k .

Download the file ace_version.tgz from any of the above locations. Unzip, untar the above file using

tar -zxvf ace_version.tgz


A directory called ace_cvs will be created. Installation complete! You can choose to work in this directory or add the directory to the matlab path using the matlab command addpath.

Getting Started
Non-Leginon Users : A demo version is available for non-leginon users.

  1. Estimation:To start using it start MATLAB  and type "acedemo"at the matlab command prompt. A Graphical User Interface (GUI) would appear. The documentation for acedemo can be accessed using the HELP button or by typing "doc acedemo" at the command prompt. The same help is also available at  ACE DEMO Documentation 
  2. Correction: After estimating the parameters of the CTF using leginon_ace_gui, the correction can be done by typing "acedemo_correct"; at the matlab command prompt. The documentation for the GUI can be accessed using the HELP button or by typing "doc acedemo_correct" at the command prompt .  The same help is also available at  ACE DEMO CORRECT Documentation.  

Leginon Users:  

  1. Estimation: Start MATLAB and type "leginon_ace_gui" at the command prompt. The documentation for the GUI can be accessed using the HELP button or by typing "doc leginon_ace_gui" at the command prompt .  The same help is available at  LEGINON ACE Documentation .

  2. Correction: After estimating the parameters of the CTF using leginon_ace_gui, the correction can be done by typing "leginon_ace_correct"; at the matlab command prompt. The documentation for the GUI can be accessed using the HELP button or by typing "doc leginon_ace_correct" at the command prompt .  The same help is also available at  LEGIONON ACE CORRECT Documentation.  

This page can also be display by typing "doc ace" in the matlab command prompt.

© 2004-2005 Satya P. Mallick