|AP C||[Rotation Alignment - classification, unknown references ||]|
|AP RA||[Alignment - Reference free, Rotation ||]|
|AP SA||[Alignment - reference free, Shift ||]|
|AP SR||[Alignment - reference free, Shift & Rotation ||]|
|PJ 3Q||[Project - 3D volume using Eulerian angles, trilinear interpolation ||]|
|SH F||[Shift - using Fourier interpolation ||]|
|CC||[Cross Correlation ||]|
|PK M||[Peak search - Maximum]|
|First||[exp]||Experimental image number|
|Second||[ref]||Reference image number|
.REFERENCE IMAGE FILE NAME OR TEMPLATE (E.G. STK@**): REF***
[Give the template name of the existing file or series of reference image/volume(s). Each of the experimental image/volume(s) will be checked for alignment versus all of these reference image/volume(s).]
.TRANSLATION SEARCH RANGE IN X, Y, & Z (ZERO FOR ALL): 0 ,0
[The search for translation parameters will be restricted to +/- search range.' If the input is zero the whole image/volume is searched. If an input is <0, then that dimension is not searched. This allows for a one dimensional search of image shift. Note: Increasing range does NOT slow this operation.]
.NORMALIZE PEAK HEIGHT, PAD IMAGE (Y/N): N
[Normalize peak height output to range: 0...1. Normalization does not slow the calculation nor improve of accuracy. Unless specified all images/volumes will be padded to twice their original dimesions with average of the image. Padding is said to improve the alignment values depending on the structure present in the image and any periodicity within the structure. It may not help your specific image.]
.EXPERIMENTAL IMAGE FILE NAME OR TEMPLATE (E.G. STK@****): EXP***
[Give the template name of the existing file or series of experiment image/volume(s). Each of the experimental image/volume(s) will be checked for alignment versus all of the reference image/volume(s).]
.OUTPUT ALIGNMENT DOCUMENT FILE: align_param
[This is the only output produced by this operation. It contains 5 register columns for each aligned image pair:
1. Number of the experimental image/volume.
2. Number of the reference image/volume.
3. X-shift. (X translation determined.)
4. Y-shift. (Y translation determined.)
5. Z-shift. (If a volume.)
6. Peak height.
Can be used as a similarity measure.
If normalized, a self correlation should give a peak height of: 1.0