Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Yasrab R

PROVIDER: S-EPMC6839032 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

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

Yasrab Robail R Atkinson Jonathan A JA Wells Darren M DM French Andrew P AP Pridmore Tony P TP Pound Michael P MP

GigaScience 20191101 11

<h4>Background</h4>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 pre ...[more]

PMID: 31702012

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Project description:Brief fragments of sleep shorter than 15 s are defined as microsleep episodes (MSEs), often subjectively perceived as sleepiness. Their main characteristic is a slowing in frequency in the electroencephalogram (EEG), similar to stage N1 sleep according to standard criteria. The maintenance of wakefulness test (MWT) is often used in a clinical setting to assess vigilance. Scoring of the MWT in most sleep-wake centers is limited to classical definition of sleep (30 s epochs), and MSEs are mostly not considered in the absence of established scoring criteria defining MSEs but also because of the laborious work. We aimed for automatic detection of MSEs with machine learning, i.e., with deep learning based on raw EEG and EOG data as input. We analyzed MWT data of 76 patients. Experts visually scored wakefulness, and according to recently developed scoring criteria MSEs, microsleep episode candidates (MSEc), and episodes of drowsiness (ED). We implemented segmentation algorithms based on convolutional neural networks (CNNs) and a combination of a CNN with a long-short term memory (LSTM) network. A LSTM network is a type of a recurrent neural network which has a memory for past events and takes them into account. Data of 53 patients were used for training of the classifiers, 12 for validation and 11 for testing. Our algorithms showed a good performance close to human experts. The detection was very good for wakefulness and MSEs and poor for MSEc and ED, similar to the low inter-expert reliability for these borderline segments. We performed a visualization of the internal representation of the data by the artificial neuronal network performing best using t-distributed stochastic neighbor embedding (t-SNE). Visualization revealed that MSEs and wakefulness were mostly separable, though not entirely, and MSEc and ED largely intersected with the two main classes. We provide a proof of principle that it is feasible to reliably detect MSEs with deep neuronal networks based on raw EEG and EOG data with a performance close to that of human experts. The code of the algorithms (https://github.com/alexander-malafeev/microsleep-detection) and data (https://zenodo.org/record/3251716) are available.

Dataset Information

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

Publications

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

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