,rain designed as a graphical front-cild that allows easy control and interaction with tasks and programs is a new computer grams for 3D reconstruction of biological complexes using cryo-electron microscopy. Cyclops' current plug-his are designed for automated particle picking and include two new algorithms, automated carbon masking and quaternion based rotation space sampling, which are also presented here. Additional plug-ins are in the pipeline. Cyclops allows straightforward organization and visualization of all data and tasks and allows both interactive and batch-wise processing. Furthermore, it was designed for straightforward implementation in grid architectures. As a front-end to a collection of programs it provides a common interface to these programs, thus enhancing the usability of the suite and the productivity Of the User. (c) 2006 Elsevier Inc. All rights reserved.