Journal Article

FZJ-2015-06881

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png The significance of image compression in plant phenotyping applications

Minervini, M. (Corresponding author) ; Scharr, H.FZJ* ; Tsaftaris, S. A.

2015
CSIRO Publ. Collingwood, Victoria

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Please use a persistent id in citations: http://hdl.handle.net/2128/9495  doi:10.1071/FP15033

Abstract: We currently witness an increasingly higher throughput in image-based plant phenotyping experiments. The majority of imaging data are collected based on complex automated procedures, and are then post-processed to extract phenotyping related information. In this article we show that image compression used in such procedures may compromise phenotyping results and needs to be taken into account. We motivate the paper with three illuminating proof of concept experiments which demonstrate that compression (especially in its most common lossy form of JPEG) does affect measurements of plant traits and errors introduced can be high. We further systematically explore how compression affects measurement fidelity, quantified as effects on image quality as well as errors in extracted plant visual traits. To do so we evaluate a variety of image-based phenotyping scenarios, including size and color of shoots, leaf and root growth, as well as root system analysis. Overall, we find that compression has a considerable effect on several types of analyses and that proper care is necessary to ensure that such choice does not affect biological findings. In order to avoid or at least minimize introduced measurement errors, for each scenario we derive recommendations and provide guidelines on how to identify suitable compression options in practice. We also find that certain compression choices can offer beneficial returns, in terms of reducing the amount of data storage without compromising phenotyping results. This may enable even higher throughput experiments in the future.

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Contributing Institute(s):

1. Pflanzenwissenschaften (IBG-2)

Research Program(s):

1. 582 - Plant Science (POF3-582) (POF3-582)

Appears in the scientific report 2015

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Database coverage:
; ; BIOSIS Previews ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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