Step 2: Align - abria/TeraStitcher GitHub Wiki

In the Align step, TeraStitcher computes a series of displacements (one per layer: layers divide the volume along Z) for each pair of adjacent tiles.

The algorithm used by default is called MIP-NCC and it is based on the Normalized Cross-Correlation applied on the three pairs of Maximum Intensity Projections extracted from the pair of tiles to be aligned.

Prerequisites

• a volume that has been previously imported (see Import step) and the correspondent XML file descriptor produced.
• an installed TeraStitcher I/O plugin supporting your image file format. You can also write your own I/O plugin.

Inputs

• absolute path of the XML descriptor (--projin)

Other inputs (optional)

• output XML descriptor filepath (--projout)
• number of slices per layer (--subvoldim)
• data subset selection (--R0 --R1 [--C0] (https://github.com/abria/TeraStitcher/wiki/User-Interface#--c0integer) --C1 --D0 --D1)
• estimated tile overlap (--oV --oH)
• displacement search region (--sV --sH --sD)
• whether to compute images descriptors to enable subsequent SPIM artifacts removal (--restoreSPIM --restoredir)
• algorithm (--algorithm)
• image channel selection (--imin_channel)

Output

• XML descriptor saved at --projout containing a series of displacements for each pair of adjacent tiles.

Demo (command line)

terastitcher --displcompute --projin="C:/volume/xml_import.xml" --subvoldim=100

Demo (GUI)