Welcome to RootReader3D
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This site provides an introductory guide to setup, install and run RootReader3D.
RootReader3D is a Javabased^{1} image analysis tool to nondestructively measure 3D root system architecture (RSA) characteristics from plants grown in hydroponics or other artificial media. The analysis is generally applicable to a wide range of plant species. This software has been used to measure root lengths (e.g., Famoso et al., 2010; Clark et al., 2011; Famoso et al., 2011; Milner et al., 2012) and contains novel features and algorithms that enable both whole root system or specific root type characteristics to be quantified.
RootReader3D utilizes a silhouettebased backprojection algorithm (Mulayim et al., 2003; Zhu et al., 2006) to construct 3D models from preprocessed binary images of root systems. It adopts a templatematching technique (Kálmán and Attila 1999), followed by a valencedriven spatial median filter (Wang and Cheng, 2008) to generate unitwidth skeleton representations of the root models. From the 3D models, the following 12 global root traits are measured:
Name  Units  Description 

Centroid  cm  Vertical position of the center of mass of the whole root system 
Convex Hull  cm3  Volume formed by the convex areas (smallest convex set of voxels that contain all root voxels in a given slice) calculated for each horizontal slice through the whole root system 
Max Depth  cm  Maximum vertical depth of whole root system 
Max Width  cm  Maximum horizontal width of whole root system 
Maximum Roots  #  Number of roots at the 84th percentile of a sorted list of root counts from all horizontal crosssectional slices through the whole root system 
Median Roots  #  Median number of roots from root counts taken from all horizontal crosssectional slices through the whole root system 
Min Width  cm  Minimum horizontal width of whole root system 
Tip Count  #  Number of root tips in the whole root system based on root voxels in the skeleton that have only one 26connected neighbor root voxel 
TSL  cm  Total root system length based on the polyline estimation technique on root voxels in the root skeleton 
TRSV  cm3  Total root system volume 
TRSSA  cm2  Total root system surface area based on root voxel counts that are 6connected to a background voxel 
Volume Distribution  cm3/cm3  Ratio of the volume of roots contained above the onethird root system depth to the volume of roots contained below the onethird root system depth 
Based on these 12 trait measurements, the following 7 additional traits are calculated:
Name  Units  Description 

Bushiness  #/#  Ratio of maximum number of roots to median number of roots; considered a measure of root branching complexity (IyerPascuzzi et al., 2010) 
Min/Max Width  cm/cm  Ratio of minimum to maximum horizontal root width 
Max Width/Max Depth  cm/cm  Ratio of maximum root width to maximum root depth 
Solidity  cm3/cm3  Ratio of the total root volume to the volume of the convex hull 
SRL  cm/cm3  Specific root length taken as the ratio of the total root length to total root volume 
TRSSA/TRSV  cm2/cm3  Ratio of total root system surface area to total root volume 
TRSL/TRSSA  cm/cm2  Ratio of total root length to total root system surface area 

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