Plant Image Analysis Plant Image Analysis

Phytotyping4D

Federico Apelt & David Breuer @ Max Planck Institute of Molecular Plant Physiology


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Scientific article

Phytotyping4D: A light-field imaging system for non-invasive and accurate monitoring of spatiotemporal
plant growth

Federico Apelt, David Breuer, Zoran Nikoloski, Mark Stitt and Friedrich Kragler1
2015, The Plant Journal

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Description

Phytotyping4D is a non-invasive and accurate imaging system that combines a 3D light-field camera (Raytrix GmbH) with an automated pipeline, which provides validated measurements of growth, movement and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping4D is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge.

Our software was developed and optimized for grey-scale 3D light-field images of Arabidopsis thaliana, and the parameters for rosette and leaf segmentation, leaf tracking and automated leaf number classification may be adapted to other plant species.

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Overview
Operating system
windows, mac, linux,

Licence
open-source, freeware,

Measured variables
angle, surface, shape, count,

Automation level
automated,

Plant requirements
Arabidopsis,

Image requirements
jpg, tiff, png (requires two gray scale images, i.e., focus and depth images),

Export formats
txt, svg,

Other information
parameters may be adjusted for analysis of other rosette plants

Additional information

Please feel free to contact the developers if there are any questions.

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