Appion

h1. Particle Alignment

Regardless of the method eventually utilized for 3D reconstruction, a good starting point for single particle EM investigations is 2D alignment and classification of the dataset.  This type of analysis intimately acquaints the scientist with the types of particles, distribution of views, and the relative amount of "junk" contained in the dataset.

h2. General Workflow:

# [[Run Alignment]]: Align particles using reference-free or reference-based approaches.  

# [[Run Feature Analysis]]: Obtain a mathematical descriptor of the variance within the dataset.

# [[Run Particle Clustering]]: Sort the dataset into classes according to an interimage variance metric.

h2. Appion SideBar Snapshot

!http://emg.nysbc.org/attachments/158/Picture_9.png!

h2. Appion Composite Output Snapshot

!http://emg.nysbc.org/attachments/191/Picture_72.png!

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[[stacks|< Stacks]] | [[Run Alignment|Run Alignment >]]

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