The significance of image compression in plant phenotyping applications

Abstract

We are currently witnessing an increasingly higher throughput in image-based plant phenotyping experiments. The majority of imaging data are collected using complex automated procedures and are then post-processed to extract phenotyping-related information. In this article, we show that the image compression used in such procedures may compromise phenotyping results and this needs to be taken into account. We use three illuminating proof-of-concept experiments that demonstrate that compression (especially in the most common lossy JPEG form) affects measurements of plant traits and the errors introduced can be high. We also 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 colour of shoots, leaf and root growth. To show that even visual impressions can be used to assess compression effects, we use root system images as examples. Overall, we find that compression has a considerable effect on several types of analyses (albeit visual or quantitative) and that proper care is necessary to ensure that this choice does not affect biological findings. In order to avoid or at least minimise 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.