The seedling hypocotyl (juvenile stem) is controlled by many endogenous and environmental factors important to plant growth and development. Therefore, its length and shape is measured in many different experimental scenarios, e.g. studies of photoreceptor function and hormonal signaling. HYPOTrace was developed in response to the need for a more automated and accurate method that could replace commonplace manual methods of making measurements from electronic images. The theory behind the HYPOTrace method is explained in the first publication. An operational version is demonstrated in the second publication.

The HYPOTrace software is available for download and demonstrated in a video tutorial.


Wang L, Assadi AH, Spalding EP (2008) Tracing branched curvilinear structures with a novel adaptive local PCA algorithm. Proc. Int'l Conf. on Image Processing, Computer Vision, & Pattern Recognition (IPCV) 2: 557–563.

Wang L, Uilecan IV, Assadi AH, Kozmik CA, Spalding EP (2009) HYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis. Plant Physiology 149: 1632–1637.