General Resources

• Getting Started with Cryo-EM
• Cryo-EM University
• CryoEM and CryoET 101
• Cryoemcenters.org
• CryoEM Service Centers YouTube Channel
• Pacific Northwest CryoEM Center (PNCC) YouTube Channel
• National Center for CryoEM Access & Training (NCCAT) YouTube Channel
• S2C2 Stanford-SLAC CryoEM Center Workshop & Lecture Archive
• UW-Madison Cryo-EM Research Center Resources
• MRC Laboratory of Molecular Biology YouTube Channel
• Thermo Fisher Scientific Electron Microscopy YouTube Channel
• 3DEM Methods

Software

• Amira (Cryo-ET Segmentation)
• AreTomo2 (Automated Tomographic Alignment & Reconstruction)
• COOT (Atomic Model Building)
• ChimeraX (Atomic Model & Volume Analysis/Editing)
• cryoDRGN (Heterogenous Single-Particle Reconstruction)
• cryoDRGN-AI (Deep Learning Ab Initio Single-Particle Reconstruction)
• CryoSPARC (Single-Particle Reconstruction)
• Dynamo (Sub-Tomogram Averaging)
• EMAN2 (Single Particle, Image Processing, & Tomogram Segmentation)
• IMOD (Tomogram Reconstruction)
• ISOLDE (Atomic Model Building & Molecular Dynamics Simulation)
• ISONet (Tomogram Denoising, Missing-Wedge Correction, & CTF Deconvolution)
• ModelAngelo (Automated Atomic Model Building)
• PEET (Sub-Tomogram Particle Alignment & Averaging)
• Phenix (Atomic Model Building, Refinement, & Validation)
• RELION (Single-Particle Reconstruction & Sub-Tomogram Averaging)
• Rosetta (Atomic Model Building & Refinement)
• SBGrid (Structural Biology Software Package Manager)

Data Management

• Globus Connect Personal Download & Installation Instructions (Official)
• Globus Connect Personal Download & Installation Instructions (Unofficial)
• Globus Shared Collections
• Globus File Manager
• Shared Data Storage from UAB Research Computing
• Data Management in CryoSPARC
• CryoEM Movie Compression

Data Publication

• Worldwide Protein Data Bank (wwPDB) OneDep System
• Electron Microscopy Public Image Archive (EMPIAR)

Mailing Lists & Forums

• 3DEM Mailing List
• 3DEM Methods Email Notifications
• CCP-EM Mailing List
• CryoSPARC Discussion Forum

Visual Aids

• TEM Simulator
• Contrast Transfer Function (CTF) Simulator
• Optics Simulator
• Atlas of Optical Transforms

Tools & Supplies Vendors

• Electron Microscopy Sciences (EMS)
• Ted Pella
• NanoSoft Materials
• SubAngstrom
• MiTeGen
• Fisher Scientific

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