= align2d =
 ''This program will align a set of images to a reference''

== Usage ==
 align2d <fixed input> <input> <output> [fixn=<n>] [noflip] [precen] [seqali] [eulali] [pgm] [log] [edgenorm] [keepeulers]

=== Parameters ===
 || <fixed input>||Reference image||
 || <input>||Images to be aligned||
 || <output>||Output filename||
 ||[fixn=<n>]||Image number to use in fixed input stack||
 ||[noflip]||Rotational/translational alignment without flips||
 ||[precen]||No translational alignment||
 ||[seqali]||Align 1st image to ref, 2nd to 1st, 3rd to 2nd, etc.||
 ||[eulali]||Align each image to images with similar Eulers, referring to the 1st image in the file.||
 ||[pgm]||Output in pgm format, note there should only be one input in this case||
 ||[log]||Logs rotations/translations to align.log||
 ||[edgenorm]||Perform an edgenormalization of both images before alignment||
 ||[keepeulers]||Indicates that the input images have accurate Eulers which need to be preserved.||
 Typical usage: align2d proj.hed cls000.hed tst.hed

== Description ==
Pretty self explanatory. If the input is a stack, the first image is used.

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EMAN Manual page, generated Mon Jan  8 17:35:59 2007