Pheno-Deep Counter: a unified and versatile deep learning architecture for leaf counting.

Abstract

Direct observation of morphological plant traits is tedious and a bottleneck for high-throughput phenotyping. Hence, interest in image-based analysis is increasing, with the requirement for software that can reliably extract plant traits, such as leaf count, preferably across a variety of species and growth conditions. However, current leaf counting methods do not work across species or conditions and therefore may lack broad utility. In this paper, we present Pheno-Deep Counter, a single deep network that can predict leaf count in two-dimensional (2D) plant images of different species with a rosette-shaped appearance. We demonstrate that our architecture can count leaves from multi-modal 2D images, such as visible light, fluorescence and near-infrared. Our network design is flexible, allowing for inputs to be added or removed to accommodate new modalities. Furthermore, our architecture can be used as is without requiring dataset-specific customization of the internal structure of the network, opening its use to new scenarios. Pheno-Deep Counter is able to produce accurate predictions in many plant species and, once trained, can count leaves in a few seconds. Through our universal and open source approach to deep counting we aim to broaden utilization of machine learning-based approaches to leaf counting. Our implementation can be downloaded at https://bitbucket.org/tuttoweb/pheno-deep-counter.

Plant phenotyping relevance

植物画像から葉数を抽出する汎用深層学習手法を開発しており、植物フェノタイピング手法が研究の中心である。

Code and data availability

The authors explicitly deposit their Pheno-Deep Counter source code and pre-trained model in a public Bitbucket repository; the plant image datasets used (CVPPP, Cruz et al., komatsuna, Aberystwyth) are cited prior-work datasets rather than paper-specific deposits.