• Leginon Leginon is a system designed for automated collection of images from a transmission electron microscope. Instruments supported: FEI (Tecnai, Titan Krios, Polara), JEOL (3200, 3100, 2100, 1230), CCDs (TVIPS, Gatan, FEI), direct detectors (Gatan K2, FEI Falcon, Direct Electron DE12, DE20).
  • Appion Appion is a “pipeline” for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools. The underlying packages integrated into Appion include EMAN, Spider, Frealign, Imagic, XMIPP, IMOD, ProTomo, ACE, CTFFind and CTFTilt, findEM, DogPicker, TiltPicker, RMeasure, EM-BFACTOR, and Chimera. These packages must be acknowledged by appropriate citations when used within Appion.
  • 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.
  • DoGpicker Particle picker that uses difference of Gaussians (DoG) for picking particles
  • TiltPicker A specially designed particle picker for image tilt pairs.
  • Maskiton An interactive, web-based tool, for creating custom masks and performing 2D classifications on aligned single-particle EM images. Sourcecode on github.