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teamtomo.org
About the project
Contributing
A short guide to git(hub)
Screen capture
Wishlist
Theory
Cryo-electron tomography
Tilt-schemes
Tilt-series alignment
Subtomogram averaging
Preprocessing
Particle picking
Template matching
Using a supporting geometry
Subboxing
Refinement
Image processing
Walkthroughs
EMPIAR-10164 (HIV VLPs)
Download the data
2D preprocessing
Tilt-series to tomograms
Geometrical particle picking
Initial model generation
Find particles on every VLP
Particle pose optimisation
Multi-particle refinement
mini-tutorials
Dynamo
Simple subtomogram averaging
Extracting particles
Spherical vesicle picking
dtmslice
viewing controls
Interactive mask creation
computing
Python
Getting started
Virtual environments
Useful packages
dynamotable
emfile
eulerangles
mrcfile
napari
starfile
MATLAB
Adding scripts/functions to your PATH in
MATLAB
Resources
Literature
Protocols
Reviews
Schur - 2019
Lučić - 2008
Lučić - 2005
Book chapters
Subtomogram averaging from cryo-electron tomograms - Leigh 2019
Cryo-Electron Tomography and Subtomogram Averaging - Wan 2016
Fiducial Marker and Hybrid Alignment Methods for Single- and Double-axis Tomography - Mastronarde 2007
Software packages
Appion-Protomo
crYOLO
Dynamo
Starters guide
Advanced starters guide
Tilt-series alignment
PCA based classification
EMAN2
Complete tutorial
Neural-net based segmentation
emClarity
tutorial
IMOD
Tomography guide
Etomo with fiducials
Patch tracking in Etomo
Batch tilt-series alignment
M
Warp/M
NovaCTF
NovaSTA
PEET
PyTom
RELION
STOPGAP
Topaz Denoise 3D
Warp
Warp/M
repository
open issue
Index
