2017 IMOD / PEET Workshop For Cryo-tomography of Biological Specimens



An IMOD / PEET workshop sponsored by NIH (NIAID, NIBIB, and NIGMS) was held June 26 – 30, 2017 at Rocky Mountain Labs, Hamilton MT in collaboration with the University of Colorado, Boulder. Material presented in this workshop, both lectures and lab exercises, are available here. Workshop participants each received an ~300 page book containing copies of the lecture slides as well as instructions for the lab exercises. A pdf copy, suitable for printing but without cover pagess, section dividers, or Acknowledgements of the Participants Workbook is available. Links to individual lecture slide sets and lab instructions are provided below. Corresponding data directories can also be found at IMOD_Labs and PEET_Labs. Links to videos of the presentations will be added when available. To install for running on your own machine, download 2017_IMOD_PEET_Workshop.tar.bz2 to some directory <mydir>, unpack by running “tar xvjf 2017_IMOD_PEET_Workshop.tar.bz2”, and then set an environment variable WORKSHOP_HOME to <mydir>/2017_IMOD_PEET_Workshop.



Day 1

  • Principles and General Aspects of Electron Tomography

Slides


  • Alignment and Other Challenges in Reconstruction Cryotomograms with IMOD

Slides


  • Walkthrough: Building a Cryotomogram With and Without Fiducials


Lab

  • Batch Processing of Tomograms with IMOD

Slides


  • Reconstruct A Cryotomogram with BatchRunTomo


Lab



Day 2

  • Reconstructing Difficult Cryotomograms using BatchRunTomo


Lab

  • CTF Correction and With IMOD

Slides

Lab

  • Denoising Cryotomograms with IMOD

Slides


  • Walkthrough: Anisotropic Diffusion


Lab

  • SerialEM for CryoTomography

Slides


  • Using Direct Detectors with SerialEM

Slides




Day 3

  • Introduction Subvolume Averaging with PEET

Slides

Lab

  • Aligning and Averaging Isolated Particles: BPV

Slides

Lab

  • Aligning and Averaging Filaments: Microtubules

Slides

Lab

  • Symmetrization

Slides

Lab



Day 4

  • Resampling

Slides

Lab

  • Modeling Aids

Slides

Lab

  • Semi-automated Particle Picking

Slides

Lab

  • Debugging

Slides

Lab

  • Verification

Slides


  • Fourier Shell Correlation

Slides

Lab



Day 5

  • Clustering / Unsupervised Classification

Slides

Lab

  • Combining Data

Slides


  • Visualization


Lab

  • Aligning and Averaging Spikes: Influenza HA

Slides