We develop the FOCUS system, which has the main purpose to function as the interface between cryo-EM data collection and cryo-EM data processing. FOCUS typically is installed on a powerful Linux computer directly adjacent to a cryo-EM instrument that collects data automatically via EPU or JADAS or SerialEM software systems. FOCUS will monitor the harddrives of the cryo-EM instrument, and once an image or a movie is recorded, FOCUS will retrieve that file and submit it to a fully automated processing pipeline, during which recorded data are analyzed (defocus, drift, resolution) and processed. FOCUS can operate in different modi: In the single particle mode, particles are picked, classified, and submitted to 2D or 3D reconstruction. In the tomography mode, recorded tilt series are drift-corrected, re-ordered (Hagen scheme), and subjected to 3D reconstruction. In the 2D crystal mode, the entire processing capability of 2dx is included and applied, which allows fully automatic processing and 3D reconstruction of membrane protein structures from 2D crystal images. FOCUS can also sort, display, and manage recorded datasets, which can become rather large (tens of TB), and the FOCUS system maintains a website to allow online tracking of the progress of data collection and data processing.

FOCUS is open-source (GPL), and available at http:/focus-em.org.