HypoTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape

HypoTrace takes time series of image files as input and output growth rate as well as hook angle measurements for Hypocotyls. The software comes with a build-in Graphical User Interface, which allows the software to be run under three modes: 1. Automatic mode with no user intervention, good for high quality images; 2. Semi-Auto mode with a little bit user intervention, good for fair quality images; 3. Manual mode, work for all images including really bad quality images. The three modes are designed to effectively detect the cotyledons bifurcation point under all conditions.

Downloading HypoTrace

To use HypoTrace, please download and install MATLAB run time library for either Windows or Mac.

There are three versions of HypoTrace available for downloading.

1. Windows version
2. Mac (Intel Processor) version
3. Mac (PowerPC) version

Running HypoTrace

Unzip specific version to your computer. To run the software:

0. Prepare a resolution file for calculating correct growth rate. Here is an example file.

1. On Windows PC, double click on the HypoTrace.exe and follow the user guide

2. On Mac, open a X window (for display purpose) and type: ./run_HypoTrace.sh [MCRroot]

Replace [MCRroot] with the actual path where the run time library is installed, by default, it is: /Applications/MATLAB/MATLAB_Component_Runtime/v76

Details

HypoTrace automatically extracts growth and shape information from electronic gray-scale images of Arabidopsis (Arabidopsis thaliana) seedlings. Key to the method is the iterative application of adaptive local principal components analysis to extract a set of ordered midline points (medial axis) from images of the seedling Hypocotyl. Pixel intensity is weighted to avoid the medial axis being diverted by the cotyledons in areas where the two come in contact. An intensity feature useful for terminating the midline at the Hypocotyl apex was isolated in each image by subtracting the baseline with a robust local regression algorithm. Applying the algorithm to time series of images of Arabidopsis seedlings responding to light resulted in automatic quantification of Hypocotyl growth rate, apical hook opening, and phototropic bending with high spatiotemporal resolution.

System requirements

HypoTrace has been tested on both Windows and UNIX (both Intel processor and PowerPC). If you need other specific version, please contact the author.

References

Wang L., Uilecan I. V., Assadi A. H., Kozmik C. A., Spalding E. P., HypoTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis, Plant Physiol. 2009, 149(4), 1632-1637. PDF

Wang L., Assadi A. H., Spalding E. P., Tracing branched curvilinear structures with a novel adaptive local PCA algorithm. Proceedings of the 2008 International Conference on Image Processing, Computer Vision, and Pattern Recognition, Ed 2. CSREA Press, Athens, GA, pp 557–563. PDF