Some small improvements were put in version 0.4.1 which was released today. You can now tune some parameters to your images such as the expected maximal elongation speed. (by adding --growth=XX in the command line).
Another work using HypoPhen to assess the growth of hypocotyls has been published in the EMBO Journal. It's available at http://www.nature.com/doifinder/10.1038/emboj.2012.186
It is published in Plant Cell.
The reference is:
C. Kami, M. Hersch, M. Trevisan, T. Genoud, A. Hiltbrunner, S. Bergmann and C. Fankhauser, Nuclear phytochrome A signaling promotes phototropism in Arabidopsis, Plant Cell,
The paper describing hypoPhen has been accepted. It should be out soon
Today I uploaded the code on sourceforge