Step 1: Import - abria/TeraStitcher GitHub Wiki

You can import your volume into TeraStitcher either from a two-level hierarchy of folders or from an XML descriptor. See the Supported volume formats section for further details.

Import from two-level hierarchy of folders

Prerequisites

• a volume stored according a two-level hierarchy of folders
• an installed TeraStitcher I/O plugin supporting your image file format. You can also write your own I/O plugin.

Inputs

• absolute path of volume root folder (--volin)
• reference system (--ref1 --ref2 --ref3)
• voxel size (--vxl1 --vxl2 --vxl3)

Other inputs (optional)

• output XML descriptor filepath (--projout)
• volume format (--volin_plugin)
• whether data is sparse (--sparse_data)
• whether folders have to be re-scanned and metadata overwritten (--rescan)
• regular expression to filter image filenames (--imin_regex)
• image file format plugin (--imin_plugin --imin_plugin_params)

Output

• metadata binary file mdata.bin stored in the volume root folder
• XML descriptor saved at --projout
• 2D image named test_middle_slice and stored in the volume root folder. It contains a slice that spans the whole XY plane at Z=N/2 where N is the highest Z-coordinate of the volume. Here, stitching is performed quickly using the nominal stage coordinates. This result is used primarily to visually check that TeraStitcher had correctly imported the volume. For advanced users, a careful inspection of tile borders in this slice can tell which is the extent of displacements between tiles and help tuning the region of search (--sV --sH --sD)

Demo (command line)

terastitcher --import --volin="C:/volume" --ref1=y --ref2=-x --ref3=z --vxl1=0.8 --vxl2=0.8 --vxl3=1 --volin_plugin="TiledXY|2Dseries"

Demo (GUI)

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Import from XML descriptor

Prerequisites

• an XML descriptor.
• 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)

Same as Import from two-level hierarchy of folders.

Output

Same as Import from two-level hierarchy of folders.

Demo (command line)

terastitcher --import --projin="C:/volume/xml_import.xml" 

Demo (GUI)