bdv-utils

Commands

Convert Tiff Slices to XML/HDF5

Loads Tiff slices from the specified input folder and saves them in BigDataViewer format.

ImageJ user interface

ImageJ Macro

run("Convert Tiff Slices to XML/HDF5", "inputfolder=/Users/tischer/Desktop/Tiff-slices xmloutputpath=/Users/tischer/Desktop/bdv.xml voxelunit=micrometer voxelsizex=0.7 voxelsizey=0.7 voxelsizez=10.0");

Java

final BdvTiffPlanesWriterCommand command = new BdvTiffPlanesWriterCommand();
command.inputFolder = new File( "/Users/tischer/Desktop/Tiff-slices" );
command.voxelSizeX = 1.0;
command.voxelSizeY = 1.0;
command.voxelSizeZ = 10.0;
command.xmlOutputPath = new File( "/Users/tischer/Desktop/bdv.xml" );
command.run();

Command line

/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run "Convert Tiff Slices to XML/HDF5" "inputFolder='/Users/tischer/Desktop/Tiff-slices',xmlOutputPath='/Users/tischer/Desktop/bdv.xml',voxelUnit='micrometer',voxelSizeX='0.7',voxelSizeY='0.7',voxelSizeZ='10.0'"