Phenotiki analysis software

Update: The Phenotiki paper has been recently published on the The Plant Journal. Our team is finalising the packaging of binaries and source code, as well as the terms and conditions under which they will be released. In the meantime, you are encouraged to download the software, by filling the following   form.

Currently our paper that describes the platform is under review and the complete software will be made available as soon as possible. Upon its release it will be free to use for academic purposes and its Matlab source code will be made available to the users. We are also working towards creating pre-compiled versions that do not require a Matlab installation. Standard disclaimers of liability (that we hold none) will apply. We are working towards identifying the best license that enables the development and continuity of Phenotiki.

To obtain the software prior to its release for testing purposes please fill out this  form. A  user manual is also available.

Our software is always under development, thanks also to all the beta tester that are collaborating across the World to improve it. You may find a CHANGELOG here.

In the meantime to help people with setting up Phenotiki devices and start collecting data we make certain parts of our software solution publicly available.

Phenotiki Device Software and GUI

Detailed instructions to setup the Phenotiki device are available in the  user manual. The web-based interface to configure and operate the device from a browser is available for download as a  ZIP archive and also as a  GitHub repository.

The Phenotiki Device software is based on the open-source project raspistillWeb and is released under the GNU General Public License (GPLv3).

Standalone Leaf Annotation Tool

The Phenotiki software suite includes also a tool to annotate plant leaves. An earlier version (with fewer features) of the leaf annotation module is in the public domain. It is available for download as a  ZIP archive (stable release, version 1.0). Alternatively, you can clone the  GitHub repository, which may include more recent updates. Detailed documentation and instructions are available in the  CVPPP paper and in the  user manual. Note that this version is not updated anymore beyond fixing bugs.

The Leaf Annotation Tool is based on the open-source Graph Analysis Toolbox by Leo Grady and is therefore released under the GNU General Public License (GPLv3).

Plant image data

The download package of the Phenotiki software includes demo images of Arabidopsis that can be used to try out the software. If you are interested in obtaining the complete dataset, we have prepared a collection of benchmark datasets for image-based plant phenotyping. We provide annotated imaging data and suitable evaluation criteria for plant/leaf segmentation, detection, tracking as well as classification and regression problems. The Plant Phenotyping Datasets are available for download at a dedicated website.

Should you encounter any issues…

 — Read the FAQ

 — Ask a question on our Google Group