Quickstart# Get Started Installation CPU/GPU/TPU Support GUI Setup Troubleshooting pyFFTW CuPy Testing Support Preprocessing Motivation Background References Filtering Techniques Noise Removal Component Emphasis Frequency Filter Spectral Whitening CTF Wedge Masks References Masking Mask Design Mask Smoothing References Practical Example Using the API Using the GUI Filtering Masking References Summary Template Matching Motivation Background Practical Example Picking Ribosomes Template and Mask Generation Template Matching Parameter Comparison Remarks on Tomogram Preprocessing References Fitting Atomic Structures Alignment of Densities Configuration Input Performance Accuracy Computation Cluster Execution SLURM (EMBL) CPU Execution GPU Execution References Summary Postprocessing Motivation Background Template Matching Output Practical Example Obtaining a Particle List Refinement Masking Manual Background Correction Validation Integrations References Summary Integrations RELION Example References IMOD Miscellaneous Contribute Code Style and Guidelines Feedback and Review Issues Bugs Features License Software License Agreement (Academic Use Only) PREAMBLE 1. Licensed Software 2. Rights of Use 3. No Licensing Fee 4. No Warranty 5. Effective Date, Term and Termination 6. Confidentiality 7. Miscellaneous Confirmation