Fig 8. ImageJ macros are accessible as a toolbar for easy access but can be readily customized for different experimental protocols.

The custom tools (identified from the default suite by the green color symbols) are (left to right) ‘Import tool’ for directly importing GE Sensing Technologies volume files into ImageJ; ‘Stitching tool’ which uses peak fitting to merge sequential scans for more consistent values; ‘rootone’ segmentation tool for extracting roots and export for connectivity filter; ‘Root Metrics’ tool which reduces volume size and measures skeleton characteristics; ‘Root length density map’ tool and root branch angle macro for manually measuring branch angle.