Appion

h1. Run Alignment

In order to extract quantitative information out of the inherently low SNR data obtained by EM, 2D averaging must be applied to homogenous subsets of single particles.  This requires the single particles to be brought into alignment with one another, so that the signal of common motifs is amplified.  Alignment protocols typically operate by shifting, rotating, and mirroring each particle in the data set in order to find the orientation of particle A that maximizes a similarity function with particle B.  Depending upon the existence of templates obtained from a priori information about the specimen, particle alignment algorithms are separated into reference-free and reference-based approaches.

h2. Reference-Free Alignment

# [[Xmipp Maximum Likelihood Alignment]]

# [[Spider Reference-free Alignment]]

h2. Reference-Based Alignment

# [[Spider Reference-based Alignment]]

# [[IMAGIC Multi Reference Alignment (MRA)]]

# [[Ed's Iteration Alignment]]

# [[Xmipp Reference-based Maximum Likelihood Alignment]]

h2. Notes, Comments, and Suggestions:

!http://emg.nysbc.org/attachments/277/Picture_81.png!

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[[Particle_Alignment|<Particle Alignment]] | [[Run Feature Analysis|Run Feature Analysis >]]

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