PhenoPhyte Home Page

Overview

PhenoPhyte is an application that allows plant area to be calculated from photos of Arabidopsis rosettes taken using a defined imaging protocol. Although developed and optimized for use with Arabidopsis rosettes, it can be used with rosettes or detached leaves from other species.

The application can quantify plant growth by taking a series of images over time and herbivory using before and after images. Images must include a color checker (like the Gretag Macbeth Mini Color Checker) so that image normalization can be automatically performed to correct for color variations (due to differences in lighting, camera, lens, etc) and to standardize the images with respect to pixel size. Please see the user guide for detailed instructions for taking the photos.

PhenoPhyte will allow you to choose the kind of experiment you are running, upload images, and preview computational results before job submission. You will need to complete a free registration page to begin. You will receive an email with a link to results once processing is complete. You will need to promptly download your results because results will be only be available for one week following their calculation.

User Manual

Click here to download a copy of the PhenoPhyte User Manual. This document contains a wealth of useful information about how PhenoPhyte works, explanations of tunable parameters, and hints and tips for tuning and optimizing those parameters.

Sample Experiments

We provide 3 small sample experiments (images and parameter suggestions) for users who are new to PhenoPhyte. This can help new users to become acquainted with PhenoPhyte.
  • Sample 1: This contains 2 images (a before and after image) from a herbivory experiment with detached leaves from Brassica rapa. Each image contains 6 leaves. Click here to download the images as well as parameter suggestions for processing these images.

  • Sample 2: This contains 4 images from a growth experiment with Arabidopsis thaliana rosettes. Each image contains 6 pots. Click here to download the images as well as parameter suggestions for processing these images.

  • Sample 3: This contains 2 images (a before and after image) from a choice assay with herbivory, again involving Arabidopsis thaliana rosettes. Each image contains 6 pots, with each pot containing 2 plants. Click here to download the images as well as parameter suggestions for processing these images.