Software¶

• ACE Automated CTF Estimation

• 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.

• Appion 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.

• DoGpicker Particle picker that uses difference of Gaussians (DoG) for picking particles

• FindEM Fast local correlation function particle picker

• EMTEM Environment Monitoring for Transmission Electron Microscopy

• Leginon 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.

• OptiMod A general, automated procedure for reconstructing and optimizing 3D models using common-lines methodologies.

• pyScope A Python extension for controlling Transmission Electron Microscopes and CCD cameras.

• TiltPicker A specially designed particle picker for image tilt pairs.

• Viewit A multidimensional image processing package.

• XMRBS-Scheduler A web based facilities scheduler

• Protomo 2.0 Tomography - Tilt Series Aligner