HypoPhen

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Note that this executable is for the standard x86 (32 bits) architectures. Let [[User:Micha  |  Micha]] know if you need it for a 64 bits architecture.  
 
Note that this executable is for the standard x86 (32 bits) architectures. Let [[User:Micha  |  Micha]] know if you need it for a 64 bits architecture.  
  
There is also a [[Media:hypoPhen.dmg.zip | dmg]] file for MacOS, but it still requires testing.  
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There is also a dmg file for MacOS, but it is still in the making.  
  
 
The [[Media:hypoPhenManual.pdf | manual ]] explains how to install and use the software.
 
The [[Media:hypoPhenManual.pdf | manual ]] explains how to install and use the software.

Revision as of 11:35, 18 January 2012

Contents

Introduction

screenshot

Hypophen is an open-source 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.


Movies

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. Here is another movie showing the analysis from scratch of the 12 example images of 5 hypocotyls, including the manual calibration procedure.

Prerequisite

Hypophen works on Linux, Mac OS X version 10.6 or later and Windows.

For Linux and Mac, 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.

Windows user can directly download the executable file and launch it from the command prompt

Download

The C++ source code (version 0.3) is available here: Media:hypophen.tar.gz. The code is also available on sourceforge

The windows executable (along with required dlls) for Windows 7 is here: Media:HypoPhen_win.zip. Note that this executable is for the standard x86 (32 bits) architectures. Let Micha know if you need it for a 64 bits architecture.

There is also a dmg file for MacOS, but it is still in the making.

The manual explains how to install and use the software.

You can also download a small set of hypocotyl images to test the software. Those images were kindly provided by Emilie Demarsy.

Related software

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

Disclaimer

This software is provided "as is", in the hope that it will be useful but without any warranty of any kind. If you use this software for research purposes, please be kind enough to mention it in your scientific publications. If you find any bug or would like to contribute to further developing this software, please write an email to Micha Hersch. The project is also available on sourceforge

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. Emilie Demarsy provided useful feedback and example of images.

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