Syntax and Tutorials
- Getting Started.
- Quickstart Tutorial -- Short SPIDER tutorial.
- Tutorial -- Longer SPIDER tutorial.
- User Manual -- Guide to Conventions and Syntax.
- Glossary of Terminology.
SPIDER Operations and Procedures
- Alphabetical List of Operations.
- Task List of Operations.
- SPIDER Procedure Index -- Examples of Procedure files.
2D Techniques
- Multivariate Data Analysis -- Overview and Procedures.
- Contrast Transfer Function Correction.
- Particle Picking/Boxing from Micrographs.
- Particle Alignment -- Strategies.
- Reference-free Alignment -- Theory.
- Supervised vs Unsupervised Classification.
- Classification and Clustering -- Tutorial.
- Supervised classification -- Procedures.
- Segmentation of Images -- Procedures.
- Contrast Transfer Function Correction -- Procedures.
- Frame Alignment with Direct Capture Cameras. -- Procedures.
- Using Relion with SPIDER data -- Protocol.
- Using SPIDER with Relion data -- Protocol.
3D Techniques
- Electron Tomography -- Procedures.
- Single Particle 3D Reconstruction (SPR) -- Philosophy.
- Single particle 3D Reconstruction -- Strategies.
- Creating Initial SPR Using Random Conical Tilt -- Protocol.
- SPR Using Projection Matching - Albany -- Protocol.
- SPR Using Projection Matching - Brno -- Protocol.
- SPR of Objects with Icosahedral Symmetry -- Protocol.
- Particle Verification using Classification -- Protocol.
- Segmentation of Volumes -- Procedures.
- Segmentation of RNA & Protein from a Ribosome -- Procedures.
- Segmentation of Ligands Using a Difference Map -- Procedures.
- Amplitude Falloff Correction -- Using low-angle X-ray scattering data -- Procedures.
File Formats and Conventions.
- SPIDER image/volume file -- Description.
- SPIDER Fourier transform file -- Description.
- SPIDER document file -- Description.
- SPIDER Euler angles -- Conventions.
SPIDER Installation.
SPIRE, SPIDER's Python tools and MPI Parallel Usage.
- Spire -- SPIDER Reconstruction Engine.
- Python tools -- for Analyzing or Preparing data.
- MPI Parallel Use.
Web -- Graphics Interface for SPIDER.
- Web documentation.
- Web Installation on Linux.
- JWeb -- Java implementation of Web.