Page Index - cianfrocco-lab/Old-school-processing GitHub Wiki

97 page(s) in this GitHub Wiki:

• Home
• Workflows
• Information for IT administrators
• 2D classification
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• 3D classification & refinement
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• 3D reconstruction of individual 2D class averages for RCT OTR
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• Analysis
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• Auto Align (Neural network)
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• Best practices in processing EM data
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• Boxer manual picking
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• Code repository vs. Wiki vs. Issues
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• Continuing Relion job
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• Converting between file types
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• Creating a new user account
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• e2boxer.py manual picking
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• Estimating the CTF
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• Extracting particles outside of Relion
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• Extracting particles using Relion
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• Filtering, thresholding, masking 3D models
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• Getting started
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• Introduction to GitHub & wiki
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• Issue Question Discussion tracking via Issues
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• IT Administrators
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• Making a particle stack
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• Manipulating images
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• Manual particle picking
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• Manual tilt pair particle picking
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• Manual vs. automatic particle picking
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• Model bias
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• Negative stain EM workflow
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• Opening particle stacks and images
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• Particle normalization
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• Particle picking guidelines
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• Particle stacks vs. single images
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• Picking a box size & pixel size for particle processing
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• Python programs & the command line interface
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• RCT OTR overall workflow
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• Relion 2D classification (Maximum likelihood)
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• Relion 3D classification
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• Relion 3D refinement
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• Relion post processing
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• Removing junk from your data
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• Searching this wiki for help
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• Semi automated tilt pair particle picking
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• Signature
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• Spider 3D refinement
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• SWARM in e2boxer.py
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• Theoretical foundations for electron microscopy & image processing
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• Using Relion for data processing
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• What is GitHub?
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