Cryo-EM : Tomography and Subtomogram Averaging

Description

Cryo-electron tomography combined with subtomogram averaging (STA) has transformed our ability to study macromolecular structures within their native cellular environments at molecular resolution. Recent advances in instrumentation and analysis software have accelerated progress in this field, while simultaneously creating new challenges in handling increasingly large and complex datasets.

This course is designed to prepare participants to navigate these challenges with confidence. Through a series of interactive, hands-on sessions, attendees will learn how to process large-scale data efficiently using Scipion—an integrative framework that enables seamless combination of multiple software packages across the entire processing pipeline, making it possible to cross-validate results within a single, intuitive environment.

Key Topics

• Optimizing workflows from raw movie frames to tomogram reconstruction
• Signal enhancement through reconstruction and restoration methods
• Particle picking using a variety of strategies
• Subtomogram averaging across different particle types
• Refinement of tilt-series alignment and contrast transfer function (CTF) estimation
• Membrane segmentation and integration with subtomogram averaging results
• Customizing workflows and tools for challenging STA cases
• Visualization and presentation of STA results in ChimeraX, including mapping back to cellular contexts and animated movie generation

Practical Information

The course emphasizes hands-on learning, complemented by concise theoretical lectures. Participants will work directly with real datasets using both local workstations and high-performance computing clusters at the Institut Pasteur.

Training will incorporate a variety of software tools, including Scipion, Relion, Dynamo, Eman, IMOD, Warp, and others. Attendees are encouraged to bring their own datasets for tailored feedback.

Learning pathway for this course:

   Introduction Course: Cryo-EM  (optional - good to haveor equivalent experience)
   Intermediate Course: Cryo-EM: Single Particle Imaging (Cryo-EM SPI)    (optional - good to have  or equivalent experience)
   Intermediate Course: Image Processing for Electron Microscopy/Tomography (Cryo-EM – IPEM)   (prerequisite course or justified equivalent experience)