Step 6: Merge - abria/TeraStitcher GitHub Wiki

In this step, TeraStitcher merges all tiles in a multiresolution representation suited for further processing and visualization. Optionally, TeraStitcher can also produce one big image file (at the original resolution) where all data are stored.

A blending function is applied along tile borders to ensure a smooth transition between adjacent overlapping tiles.

Prerequisites

• an XML descriptor generated by the Place step or, alternatively, an XML descriptor containing tile positions.

Since this step only needs tile positions, you can also skip steps 2, 3, 4, 5 and provide your tile positions in the XML descriptor or, alternatively, trust the default values computed from nominal stage coordinates.

Inputs

• absolute path of the XML descriptor (--projin)
• absolute path of the output volume folder (--volout)

Other inputs (optional)

• output volume and image format (--volout_plugin --slicewidth --sliceheight --slicedepth --imout_format --imout_depth --imout_plugin)
• resolutions to be produced (--resolutions)
• data subset selection (--R0 --R1 [--C0] (https://github.com/abria/TeraStitcher/wiki/User-Interface#--c0integer) --C1 --D0 --D1)
• image channel selection (--imin_channel)
• blending algorithm (--algorithm)
• whether to exclude nonstitchable tiles from merging (--stitchablesonly)
• whether to apply SPIM artifacts removal (--restoreSPIM --restoredir)

Output

• stitched image saved at --volout.

Demo (command line)

Case 1

Save the stitched image into a 5-level multiresolution representation. Each level is stored according to a 3D tiled format with tile dimensions 512x512x256 along XYZ and image format tif.

terastitcher --merge --projin="C:/volume/xml_merging.xml" --volout="C:/volume.stitched" --resolutions=01234  --volout_plugin="TiledXY|3Dseries" --imout_format="tif" --slicewidth=512 --sliceheight=512 --slicedepth=256

Case 2

Save the stitched image into a 5-level multiresolution representation. Each level is stored into a big 3D tiff file.

terastitcher --merge --projin="C:/volume/xml_merging.xml" --volout="C:/volume.stitched" --resolutions=01234  --volout_plugin="TiledXY|3Dseries" --imout_format="tif"

Case 3

Save the stitched image into one big 3D tiff (no multiresolution).

terastitcher --merge --projin="C:/volume/xml_merging.xml" --volout="C:/volume.stitched" --volout_plugin="TiledXY|3Dseries" --imout_format="tif"

Case 4

Save the stitched image into a series of 3D tiffs each composed by 512 slices (no multiresolution).

terastitcher --merge --projin="C:/volume/xml_merging.xml" --volout="C:/volume.stitched" --volout_plugin="TiledXY|3Dseries" --imout_format="tif" --slicedepth=512

Case 5

Save the stitched image into a series of big 2D tiffs (no multiresolution).

terastitcher --merge --projin="C:/volume/xml_merging.xml" --volout="C:/volume.stitched" --volout_plugin="TiledXY|2Dseries" --imout_format="tif"

Demo (GUI)