HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape
Here is a tutorial on youtube to get started.
For example use cases, please check the following paper:
Wang, Liya, Ioan Vlad Uilecan, Amir H. Assadi, Christine A. Kozmik, and Edgar P. Spalding. "HYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis." Plant physiology 149, no. 4 (2009): 1632-1637. Link
For the tracing algorithm, please check the following paper:
Wang, Liya, Amir H. Assadi, and Edgar Spalding. "Tracing Branched Curvilinear Structures with a Novel Adaptive Local PCA Algorithm." In IPCV, pp. 557-563. 2008. Link