RootflowRT v.2.8

Tip Tracking

About Tip Tracking

Tip tracking is a utility created by Hai Jiang for use by the Baskin Lab to track the velocity around the quiescent center of a growing root.

Input Images

Tip tracking expects the same image conventions as RootflowRTv.2.8. For more information see Input Image Requirements. The main difference will be all frames will be in one stack and every frame is taken every 10 seconds. It may take 18 frames or 180 frames depending on the speed of root growth and image quality. Eg. Stack0001Frame0001…Stack0001Frame0018

Other Input Data

In addition to the image files, the software needs three additional parameters. The first is the coordinate location of the quiescent center (QC) of the center frame of the stack. This would be the 9^th frame of 18, or the 60^th of 120 frames. The second parameter is a window dimension in pixels where 75 x 40 is usual. This window is used to set the window area to average velocity over. The third input parameter is the margin distance between the edge and the QC. A margin of 10 seems to work in most cases.

Input Files

Instead of manually entering these parameters at the command line, an input file can be created.

Running Tip Tracking on Baskin Lab Computers

In the bin directory of the lab computer there should be a script file named "runtip2". At the command line in the Terminal program the following command needs to be entered to run the tip tracking program.

After the runtip2 command, the user must give the working directory where the image files are located, next is the name of the image files relative to that working directory. This can be the "." which indicates the current directory. The software needs to know the filenames relative to the given working directory, such as "Stack0001Frame0". The "1 18" indicates the number of the frames to be analyzed, which in this case Stack0001Frame0001.tif to Stack0001Frame0018.tif. After that, if the images have a filename extension, it can be included here. The "< input.txt " will redirect the program input to the named file relative to the working directory. Eg.

runtip2 . "Stack0001Frame0" 1 18 ".tif" < input.txt

or

runtip2 /Users/baskinLab/work/ "stack0001frame0" 1 180

In the second case, since no input files is specified, the program will request the user enter the required input data at the command line.

Output Files Produced after Successful Analysis

After analysis, an output text file will be created in the working directory.

The end of the output file contains four columns. The first column represents the middle frame. The second is the average total velocity, while the third and fourth are the x, y components of the average velocity of tip zone.