Deep learning-based phenotyping for genome wide association studies of sudden death syndrome in soybean

Using a reliable and accurate method to phenotype disease incidence and severity is essential to unravel the complex genetic architecture of disease resistance in plants, and to develop disease resistant cultivars. Genome-wide association studies (GWAS) involve phenotyping large numbers of accessions, and have been used for a myriad of traits. In field studies, genetic accessions are phenotyped across multiple environments and replications, which takes a significant amount of labor and resources. Deep Learning (DL) techniques can be effective for analyzing image-based tasks; thus DL methods are becoming more routine for phenotyping traits to save time and effort. This research aims to conduct GWAS on sudden death syndrome (SDS) of soybean [Glycine max L. (Merr.)] using disease severity from both visual field ratings and DL-based (using images) severity ratings collected from 473 accessions. Images were processed through a DL framework that identified soybean leaflets with SDS symptoms, and then quantified the disease severity on those leaflets into a few classes with mean Average Precision of 0.34 on unseen test data. Both visual field ratings and image-based ratings identified significant single nucleotide polymorphism (SNP) markers associated with disease resistance. These significant SNP markers are either in the proximity of previously reported candidate genes for SDS or near potentially novel candidate genes. Four previously reported SDS QTL were identified that contained a significant SNPs, from this study, from both a visual field rating and an image-based rating. The results of this study provide an exciting avenue of using DL to capture complex phenotypic traits from images to get comparable or more insightful results compared to subjective visual field phenotyping of traits for disease symptoms.

Fusing Self-Organized Neural Network and Keypoint Clustering for Localized Real-Time Background Subtraction

Moving object detection in video streams plays a key role in many computer vision applications. In particular, separation between background and foreground items represents a main prerequisite to carry out more complex tasks, such as object classification, vehicle tracking, and person re-identification. Despite the progress made in recent years, a main challenge of moving object detection still regards the management of dynamic aspects, including bootstrapping and illumination changes. In addition, the recent widespread of Pan-Tilt-Zoom (PTZ) cameras has made the management of these aspects even more complex in terms of performance due to their mixed movements (i.e. pan, tilt, and zoom). In this paper, a combined keypoint clustering and neural background subtraction method, based on Self-Organized Neural Network (SONN), for real-time moving object detection in video sequences acquired by PTZ cameras is proposed. Initially, the method performs a spatio-temporal tracking of the sets of moving keypoints to recognize the foreground areas and to establish the background. Then, it adopts a neural background subtraction, localized in these areas, to accomplish a foreground detection able to manage bootstrapping and gradual illumination changes. Experimental results on three well-known public datasets, and comparisons with different key works of the current literature, show the efficiency of the proposed method in terms of modeling and background subtraction.

Spatio-Temporal Attention Model for Foreground Detection in Cross-Scene Surveillance Videos

Foreground detection is an important theme in video surveillance. Conventional background modeling approaches build sophisticated temporal statistical model to detect foreground based on low-level features, while modern semantic/instance segmentation approaches generate high-level foreground annotation, but ignore the temporal relevance among consecutive frames. In this paper, we propose a Spatio-Temporal Attention Model (STAM) for cross-scene foreground detection. To fill the semantic gap between low and high level features, appearance and optical flow features are synthesized by attention modules via the feature learning procedure. Experimental results on CDnet 2014 benchmarks validate it and outperformed many state-of-the-art methods in seven evaluation metrics. With the attention modules and optical flow, its F-measure increased 9% and 6% respectively. The model without any tuning showed its cross-scene generalization on Wallflower and PETS datasets. The processing speed was 10.8 fps with the frame size 256 by 256.

Real-Time Object Tracking with Template Tracking and Foreground Detection Network

In this paper, we propose a fast and accurate deep network-based object tracking method, which combines feature representation, template tracking and foreground detection into a single framework for robust tracking. The proposed framework consists of a backbone network, which feeds into two parallel networks, TmpNet for template tracking and FgNet for foreground detection. The backbone network is a pre-trained modified VGG network, in which a few parameters need to be fine-tuned for adapting to the tracked object. FgNet is a fully convolutional network to distinguish the foreground from background in a pixel-to-pixel manner. The parameter in TmpNet is the learned channel-wise target template, which initializes in the first frame and performs fast template tracking in the test frames. To enable each component to work closely with each other, we use a multi-task loss to end-to-end train the proposed framework. In online tracking, we combine the score maps from TmpNet and FgNet to find the optimal tracking results. Experimental results on object tracking benchmarks demonstrate that our approach achieves favorable tracking accuracy against the state-of-the-art trackers while running at a real-time speed of 38 fps.

Foreground Detection with Deeply Learned Multi-Scale Spatial-Temporal Features

Foreground detection, which extracts moving objects from videos, is an important and fundamental problem of video analysis. Classic methods often build background models based on some hand-craft features. Recent deep neural network (DNN) based methods can learn more effective image features by training, but most of them do not use temporal feature or use simple hand-craft temporal features. In this paper, we propose a new dual multi-scale 3D fully-convolutional neural network for foreground detection problems. It uses an encoder–decoder structure to establish a mapping from image sequences to pixel-wise classification results. We also propose a two-stage training procedure, which trains the encoder and decoder separately to improve the training results. With multi-scale architecture, the network can learning deep and hierarchical multi-scale features in both spatial and temporal domains, which is proved to have good invariance for both spatial and temporal scales. We used the CDnet dataset, which is currently the largest foreground detection dataset, to evaluate our method. The experiment results show that the proposed method achieves state-of-the-art results in most test scenes, comparing to current DNN based methods.

Depth-Based Detection of Standing-Pigs in Moving Noise Environments

In a surveillance camera environment, the detection of standing-pigs in real-time is an important issue towards the final goal of 24-h tracking of individual pigs. In this study, we focus on depth-based detection of standing-pigs with “moving noises”, which appear every night in a commercial pig farm, but have not been reported yet. We first apply a spatiotemporal interpolation technique to remove the moving noises occurring in the depth images. Then, we detect the standing-pigs by utilizing the undefined depth values around them. Our experimental results show that this method is effective for detecting standing-pigs at night, in terms of both cost-effectiveness (using a low-cost Kinect depth sensor) and accuracy (i.e., 94.47%), even with severe moving noises occluding up to half of an input depth image. Furthermore, without any time-consuming technique, the proposed method can be executed in real-time.

Comparative Evaluation of Background Subtraction Algorithms in Remote Scene Videos Captured by MWIR Sensors

Background subtraction (BS) is one of the most commonly encountered tasks in video analysis and tracking systems. It distinguishes the foreground (moving objects) from the video sequences captured by static imaging sensors. Background subtraction in remote scene infrared (IR) video is important and common to lots of fields. This paper provides a Remote Scene IR Dataset captured by our designed medium-wave infrared (MWIR) sensor. Each video sequence in this dataset is identified with specific BS challenges and the pixel-wise ground truth of foreground (FG) for each frame is also provided. A series of experiments were conducted to evaluate BS algorithms on this proposed dataset. The overall performance of BS algorithms and the processor/memory requirements were compared. Proper evaluation metrics or criteria were employed to evaluate the capability of each BS algorithm to handle different kinds of BS challenges represented in this dataset. The results and conclusions in this paper provide valid references to develop new BS algorithm for remote scene IR video sequence, and some of them are not only limited to remote scene or IR video sequence but also generic for background subtraction. The Remote Scene IR dataset and the foreground masks detected by each evaluated BS algorithm are available online: https://github.com/JerryYaoGl/BSEvaluationRemoteSceneIR.

Illumination and Reflectance Estimation with its Application in Foreground Detection

In this paper, we introduce a novel approach to estimate the illumination and reflectance of an image. The approach is based on illumination-reflectance model and wavelet theory. We use a homomorphic wavelet filter (HWF) and define a wavelet quotient image (WQI) model based on dyadic wavelet transform. The illumination and reflectance components are estimated by using HWF and WQI, respectively. Based on the illumination and reflectance estimation we develop an algorithm to segment sows in grayscale video recordings which are captured in complex farrowing pens. Experimental results demonstrate that the algorithm can be applied to detect the domestic animals in complex environments such as light changes, motionless foreground objects and dynamic background.

Sudden event recognition: a survey

Event recognition is one of the most active research areas in video surveillance fields. Advancement in event recognition systems mainly aims to provide convenience, safety and an efficient lifestyle for humanity. A precise, accurate and robust approach is necessary to enable event recognition systems to respond to sudden changes in various uncontrolled environments, such as the case of an emergency, physical threat and a fire or bomb alert. The performance of sudden event recognition systems depends heavily on the accuracy of low level processing, like detection, recognition, tracking and machine learning algorithms. This survey aims to detect and characterize a sudden event, which is a subset of an abnormal event in several video surveillance applications. This paper discusses the following in detail: (1) the importance of a sudden event over a general anomalous event; (2) frameworks used in sudden event recognition; (3) the requirements and comparative studies of a sudden event recognition system and (4) various decision-making approaches for sudden event recognition. The advantages and drawbacks of using 3D images from multiple cameras for real-time application are also discussed. The paper concludes with suggestions for future research directions in sudden event recognition.

Robust foreground detection: a fusion of masked grey world, probabilistic gradient information and extended conditional random field approach

Foreground detection has been used extensively in many applications such as people counting, traffic monitoring and face recognition. However, most of the existing detectors can only work under limited conditions. This happens because of the inability of the detector to distinguish foreground and background pixels, especially in complex situations. Our aim is to improve the robustness of foreground detection under sudden and gradual illumination change, colour similarity issue, moving background and shadow noise. Since it is hard to achieve robustness using a single model, we have combined several methods into an integrated system. The masked grey world algorithm is introduced to handle sudden illumination change. Colour co-occurrence modelling is then fused with the probabilistic edge-based background modelling. Colour co-occurrence modelling is good in filtering moving background and robust to gradual illumination change, while an edge-based modelling is used for solving a colour similarity problem. Finally, an extended conditional random field approach is used to filter out shadow and afterimage noise. Simulation results show that our algorithm performs better compared to the existing methods, which makes it suitable for higher-level applications.