Automated recovery of 3D models of plant shoots from multiple colour images

Increased adoption of the systems approach to biological research has focussed attention on the use of quantitative models of biological objects. This includes a need for realistic 3D representations of plant shoots for quantification and modelling. Previous limitations in single or multi-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present a fully automatic approach to image-based 3D plant reconstruction that can be achieved using a single low-cost camera. The reconstructed plants are represented as a series of small planar sections that together model the more complex architecture of the leaf surfaces. The boundary of each leaf patch is refined using the level set method, optimising the model based on image information, curvature constraints and the position of neighbouring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed, and as such is applicable to a wide variety of plant species and topologies, and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on datasets of wheat and rice plants, as well as a novel virtual dataset that allows us to compute quantitative measures of reconstruction accuracy. The output is a 3D mesh structure that is suitable for modelling applications, in a format that can be imported in the majority of 3D graphics and software packages

Three Dimensional Root CT Segmentation Using Multi-Resolution Encoder-Decoder Networks

© 1992-2012 IEEE. We address the complex problem of reliably segmenting root structure from soil in X-ray Computed Tomography (CT) images. We utilise a deep learning approach, and propose a state-of-the-art multi-resolution architecture based on encoder-decoders. While previous work in encoder-decoders implies the use of multiple resolutions simply by downsampling and upsampling images, we make this process explicit, with branches of the network tasked separately with obtaining local high-resolution segmentation, and wider low-resolution contextual information. The complete network is a memory efficient implementation that is still able to resolve small root detail in large volumetric images. We compare against a number of different encoder-decoder based architectures from the literature, as well as a popular existing image analysis tool designed for root CT segmentation. We show qualitatively and quantitatively that a multi-resolution approach offers substantial accuracy improvements over a both a small receptive field size in a deep network, or a larger receptive field in a shallower network. We then further improve performance using an incremental learning approach, in which failures in the original network are used to generate harder negative training examples. Our proposed method requires no user interaction, is fully automatic, and identifies large and fine root material throughout the whole volume

Image-based 3D canopy reconstruction to determine potential productivity in complex multi-species crop systems

Background and Aims: Intercropping systems contain two or more species simultaneously in close proximity. Due to contrasting features of the component crops, quantification of the light environment and photosynthetic productivity is extremely difficult. However it is an essential component of productivity. Here, a low-tech but high resolution method is presented that can be applied to single and multi-species cropping systems, to facilitate characterisation of the light environment. Different row layouts of an intercrop consisting of Bambara groundnut (Vigna subterranea (L.) Verdc.) and Proso millet (Panicum miliaceum) have been used as an example and the new opportunities presented by this approach have been analysed. Methods: Three-dimensional plant reconstruction, based on stereocameras, combined with ray-tracing was implemented to explore the light environment within the Bambara groundnut-Proso millet intercropping system and associated monocrops. Gas exchange data was used to predict the total carbon gain of each component crop. Key Results: The shading influence of the tall Proso millet on the shorter Bambara groundnut results in a reduction in total canopy light interception and carbon gain. However, the increased leaf area index (LAI) of Proso millet, higher photosynthetic potential due to the C4 pathway and sub-optimal photosynthetic acclimation of Bambara groundnut to shade means that increasing the number of rows of millet will lead to greater light interception and carbon gain per unit ground area, despite Bambara groundnut intercepting more light per unit leaf area. Conclusions: Three-dimensional reconstruction combined with ray tracing provides a novel, accurate method of exploring the light environment within an intercrop that does not require difficult measurements of light interception and data-intensive manual reconstruction, especially for such systems with inherently high spatial possibilities. It provides new opportunities for calculating potential productivity within multispecies cropping systems; enables the quantification of dynamic physiological differences between crops grown as monoculture and those within intercrops or; enables the prediction of new productive combinations of previously untested crops

Approaches to three-dimensional reconstruction of plant shoot topology and geometry

There are currently 805 million people classified as chronically undernourished, and yet the World’s population is still increasing. At the same time, global warming is causing more frequent and severe flooding and drought, thus destroying crops and reducing the amount of land available for agriculture. Recent studies show that without crop climate adaption, crop productivity will deteriorate. With access to 3D models of real plants it is possible to acquire detailed morphological and gross developmental data that can be used to study their ecophysiology, leading to an increase in crop yield and stability across hostile and changing environments. Here we review approaches to the reconstruction of 3D models of plant shoots from image data, consider current applications in plant and crop science, and identify remaining challenges. We conclude that although phenotyping is receiving an increasing amount of attention – particularly from computer vision researchers – and numerous vision approaches have been proposed, it still remains a highly interactive process. An automated system capable of producing 3D models of plants would significantly aid phenotyping practice, increasing accuracy and repeatability of measurements

Addressing multiple salient object detection via dual-space long-range dependencies

Salient object detection plays an important role in many downstream tasks. However, complex real-world scenes with varying scales and numbers of salient objects still pose a challenge. In this paper, we directly address the problem of detecting multiple salient objects across complex scenes. We propose a network architecture incorporating non-local feature information in both the spatial and channel spaces, capturing the long-range dependencies between separate objects. Traditional bottom-up and non-local features are combined with edge features within a feature fusion gate that progressively refines the salient object prediction in the decoder. We show that our approach accurately locates multiple salient regions even in complex scenarios. To demonstrate the efficacy of our approach to the multiple salient objects problem, we curate a new dataset containing only multiple salient objects. Our experiments demonstrate the proposed method presents state-of-the-art results on five widely used datasets without any pre-processing and post-processing. We obtain a further performance improvement against competing techniques on our multi-objects dataset. The dataset and source code are available at: https://github.com/EricDengbowen/DSLRDNe

A patch-based approach to 3D plant shoot phenotyping

The emerging discipline of plant phenomics aims to measure key plant characteristics, or traits, though as yet the set of plant traits that should be measured by automated systems is not well defined. Methods capable of recovering generic representations of the 3D structure of plant shoots from images would provide a key technology underpinning quantification of a wide range of current and future physiological and morphological traits. We present a fully automatic approach to image-based 3D plant reconstruction which represents plants as series of small planar sections that together model the complex architecture of leaf surfaces. The initial boundary of each leaf patch is refined using a level set method, optimising the model based on image information, curvature constraints and the position of neighbouring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed. As such it is applicable to a wide variety of plant species and topologies, and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on real images of wheat and rice plants, an artificial plant with challenging architecture, as well as a novel virtual dataset that allows us to compute distance measures of reconstruction accuracy. We also illustrate the method’s potential to support the identification of individual leaves, and so the phenotyping of plant shoots, using a spectral clustering approach

Recovering Wind-induced Plant motion in Dense Field Environments via Deep Learning and Multiple Object Tracking

Understanding the relationships between local environmental conditions and plant structure and function is critical for both fundamental science and for improving the performance of crops in field settings. Wind-induced plant motion is important in most agricultural systems, yet the complexity of the field environment means that it remained understudied. Despite the ready availability of image sequences showing plant motion, the cultivation of crop plants in dense field stands makes it difficult to detect features and characterize their general movement traits. Here, we present a robust method for characterizing motion in field-grown wheat plants (Triticum aestivum) from time-ordered sequences of red, green and blue (RGB) images. A series of crops and augmentations was applied to a dataset of 290 collected and annotated images of ear tips to increase variation and resolution when training a convolutional neural network. This approach enables wheat ears to be detected in the field without the need for camera calibration or a fixed imaging position. Videos of wheat plants moving in the wind were also collected and split into their component frames. Ear tips were detected using the trained network, then tracked between frames using a probabilistic tracking algorithm to approximate movement. These data can be used to characterize key movement traits, such as periodicity, and obtain more detailed static plant properties to assess plant structure and function in the field. Automated data extraction may be possible for informing lodging models, breeding programmes and linking movement properties to canopy light distributions and dynamic light fluctuation

Three-dimensional reconstruction of plant shoots from multiple images using an active vision system

The reconstruction of 3D models of plant shoots is a challenging problem central to the emerging discipline of plant phenomics – the quantitative measurement of plant structure and function. Current approaches are, however, often limited by the use of static cameras. We propose an automated active phenotyping cell to reconstruct plant shoots from multiple images using a turntable capable of rotating 360 degrees and camera mounted robot arm. To overcome the problem of static camera positions we develop an algorithm capable of analysing the environment and determining viewpoints from which to capture initial images suitable for use by a structure from motion technique

RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures

© The Author(s) 2019. Published by Oxford University Press. BACKGROUND: In recent years quantitative analysis of root growth has become increasingly important as a way to explore the influence of abiotic stress such as high temperature and drought on a plant's ability to take up water and nutrients. Segmentation and feature extraction of plant roots from images presents a significant computer vision challenge. Root images contain complicated structures, variations in size, background, occlusion, clutter and variation in lighting conditions. We present a new image analysis approach that provides fully automatic extraction of complex root system architectures from a range of plant species in varied imaging set-ups. Driven by modern deep-learning approaches, RootNav 2.0 replaces previously manual and semi-automatic feature extraction with an extremely deep multi-task convolutional neural network architecture. The network also locates seeds, first order and second order root tips to drive a search algorithm seeking optimal paths throughout the image, extracting accurate architectures without user interaction. RESULTS: We develop and train a novel deep network architecture to explicitly combine local pixel information with global scene information in order to accurately segment small root features across high-resolution images. The proposed method was evaluated on images of wheat (Triticum aestivum L.) from a seedling assay. Compared with semi-automatic analysis via the original RootNav tool, the proposed method demonstrated comparable accuracy, with a 10-fold increase in speed. The network was able to adapt to different plant species via transfer learning, offering similar accuracy when transferred to an Arabidopsis thaliana plate assay. A final instance of transfer learning, to images of Brassica napus from a hydroponic assay, still demonstrated good accuracy despite many fewer training images. CONCLUSIONS: We present RootNav 2.0, a new approach to root image analysis driven by a deep neural network. The tool can be adapted to new image domains with a reduced number of images, and offers substantial speed improvements over semi-automatic and manual approaches. The tool outputs root architectures in the widely accepted RSML standard, for which numerous analysis packages exist (http://rootsystemml.github.io/), as well as segmentation masks compatible with other automated measurement tools. The tool will provide researchers with the ability to analyse root systems at larget scales than ever before, at a time when large scale genomic studies have made this more important than ever

Domain Adaptation and Federated Learning for Ultrasonic Monitoring of Beer Fermentation

Beer fermentation processes are traditionally monitored through sampling and off-line wort density measurements. In-line and on-line sensors would provide real-time data on the fermentation progress whilst minimising human involvement, enabling identification of lagging fermentations or prediction of ethanol production end points. Ultrasonic sensors have previously been used for in-line and on-line fermentation monitoring and are increasingly being combined with machine learning models to interpret the sensor measurements. However, fermentation processes typically last many days and so impose a significant time investment to collect data from a sufficient number of batches for machine learning model training. This expenditure of effort must be multiplied if different fermentation processes must be monitored, such as varying formulations in craft breweries. In this work, three methodologies are evaluated to use previously collected ultrasonic sensor data from laboratory scale fermentations to improve machine learning model accuracy on an industrial scale fermentation process. These methodologies include training models on both domains simultaneously, training models in a federated learning strategy to preserve data privacy, and fine-tuning the best performing models on the industrial scale data. All methodologies provided increased prediction accuracy compared with training based solely on the industrial fermentation data. The federated learning methodology performed best, achieving higher accuracy for 14 out of 16 machine learning tasks compared with the base case model