cisTEM

cisTEM processes cryo-electron microscopy (cryo-EM) data to generate high-resolution 3D reconstructions of macromolecular complexes for structural biology.

Key Features:

• Full processing pipeline: End-to-end cryo-EM workflow including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction.
• Algorithm innovation: Incorporates newly developed algorithms alongside adapted published algorithms to improve processing of complex datasets.
• Performance optimization: Optimized to process large datasets (typically ~2,000 micrographs with 200,000–300,000 particles) on high-end CPU-based workstations within approximately half a day, achieving performance comparable to GPU-accelerated methods.
• Cluster scheduling and scalability: Supports job scheduling on large computer clusters with flexible run profiles adaptable to different computing environments.

Scientific Applications:

• Single-particle averaging: Automated processing and classification to support single-particle analysis workflows for macromolecular complexes.
• High-resolution structure determination: Generation and refinement of 3D reconstructions to elucidate molecular architectures and mechanisms at high resolution.

Methodology:

Preprocessing of raw micrograph movies for motion and artifact correction, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, followed by 3D classification and high-resolution refinement and reconstruction.