HypoPhen

Introduction

Hypophen is a software enabling the semi-automatic phenotyping of growing seedlings from time-lapse images. More precisely, it computes and records the elongation and bending of the seedlings. It is semi-automatic in the sense that manual calibration, verification and adjustments are sometimes needed. In my experience, it allows a throughput of about 50 images of 20 hypocotyls in about 10 minutes, given a reasonable image quality.

Movie

Here is a movie showing in real time an excerpt from the semi-automated processing of images of 14 hypocotyls. In those 20 seconds, five frames (70 hypocotyls) are processed.

Prerequisite

Hypophen works on Linux and Mac OS X version 10.6 or later. It needs the OpenCV library (free) and must be compiled from source, The use of CMake (also free) makes this rather straightforward. You also need a two button mouse to use the software. More details are given in the manual.

Download

The C++ source code is available here here The manual explains how to install and use the software.

Related software

Software trying to achieve similar goals include HypoTrace and HyDe both of which are matlab-based and not open-source.

Credits

Hypophen was written by Micha Hersch in collaboration with Chitose Kami and Christian Fankhauser from the Center for Integrative Genomics at the University of Lausanne. The project was initiated with the help of Ioannis Xenarios from Vital-IT and Sven Bergmann, head of the CBG. It uses the OpenCV library and some code written by Basilio Noris.

The development of this software was funded by SystemsX throught the Plant Growth project