RootflowRT v.2.8


About RootflowRT v.2.8


The Software

Dr H Jiang and Dr K Palaniappian created RootflowRT at the University of Missouri-Columbia, in collaboration with Dr T Baskin. W Sulaman implemented the graphical user interface while at the University of Massachusetts-Amherst with Dr T Baskin.


The software was designed to estimate spatial velocity profiles for growing roots of Arabidopsis thaliana at high spatial resolution. The images of roots that are best suited for analysis are those with clear focus throughout the growing root and the root"s midline is parallel to the horizontal axis of the image frame. Roots that are very curved and undulate in and out of the focal plane are not suitable for analysis.


Input Image Requirements

Images should be in .tif or .ppm format, contain 8-bit gray scale values and 640x480up to 1200x1600 in dimension. Roots are imaged as overlapping stacks throughout the tip to the maturation zone or as a single stack of just one region such as the root tip.  Overlapping between stacks should be at least 20% of the field of view.  Each root segment stack must be imaged 9 times taken over precise time intervals. Each of these 9 images is a frame in the stack.


Input Image File Names

The software expects the image files to be named according to precise conventions. In particular, the images should be named Stack00xxFrame00yy with or without filename extension such as .tif or .pgm. For example, a root may be imaged with 5 overlapping stacks with frames taken every 15s. In this case, the image files can be:












Mosaic Method Between Overlapping Stacks

This refers to the process of blending together the velocity profiles of each of the individual stacks into one complete velocity profile for the entire root. There are two ways this can be executed, 1) Moving a precise fixed distance between every stack or; 2) Taking a highly textured image of the background after the 9thframe and naming it Stack00xxBack0001 eg.Stack0006Back0001.tif.


Input Files

For each root a specially formatted input file is required that can be generated manually or with the Make Input File menu option. It should be located in the working directory.


Output Files Produced after Successful Analysis

After a successful analysis, several files will be output to the working directory. There should be diameterprune_xx.tif and pointsfitline_xx.tif files for each stack. These can be examined for quality and accuracy.


The last line of the input.txt file specifies the names of two key output files. They contain the numeric velocity data from the tensor only and robust-tensor methods. For example, Control_root2.txt and Control_root2_tensorresult.txt may be two output files that result.




The end of the output files, contain columns in three pairs. These are the resulting velocities and can be graphed by importing this as a space-delimited file into Microsoft Excel.  More information about these columns is present in the output file. The first pair represents the pixel distance from the quiescent center and the corresponding velocity at that point in pixels/frame. The second pair represents the micron distance from the QC and the corresponding velocity in microns/second.