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Step 2: Align
Mark Harfouche edited this page Jun 20, 2018
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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.
- 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.
- absolute path of the XML descriptor (
--projin
)
- 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
)
- XML descriptor saved at
--projout
containing a series of displacements for each pair of adjacent tiles.
terastitcher --displcompute --projin="C:/volume/xml_import.xml" --subvoldim=100
Wiki maintained by Alessandro Bria and Giulio Iannello.
- Quick Guide (pdf)
- TeraTools Guide (pdf)
- Stitching pipeline
- User Interface
- Supported volume formats
- Demo and batch scripts
- Built-in I/O plugins
- FAQ