Phenotyping is the process of measuring an organism's observable traits. Manual phenotyping of crops is a labor-intensive, time-consuming, costly, and error prone process. Accurate, automated, high-throughput phenotyping can relieve a huge burden in the crop breeding pipeline. In this paper, we propose a scalable, high-throughput approach to automatically count and segment panicles (heads), a key phenotype, from aerial sorghum crop imagery. Our counting approach uses the image density map obtained from dot or region annotation as the target with a novel deep convolutional neural network architecture. We also propose a novel instance segmentation algorithm using the estimated density map, to identify the individual panicles in the presence of occlusion. With real Sorghum aerial images, we obtain a mean absolute error (MAE) of 1.06 for counting which is better than using well-known crowd counting approaches such as CCNN, MCNN and CSRNet models. The instance segmentation model also produces respectable results which will be ultimately useful in reducing the manual annotation workload for future data.
While these papers used the CCNN type architecture, the popular U-net architecture has been used in @cite_19 together with a scale consistency regularizer that forces collaborative predictions from the ensemble models. The U-net model has been widely used in medical imaging. , Ronnenberger , @cite_51 use the U-net for cell tracking in bio-medical imaging. Examples of works that allow for very deep networks include @cite_6 and @cite_27 , both of which use a VGG @cite_17 type architecture. Shi @cite_6 utilize a multi-scale architecture, where a part of their network uses complex ensemble averaging to combine image density maps from models built for different scales. Li @cite_27 introduce the dilated convolution to aggregate multi-scale contextual information in the CSRNet model (see Figure ). @cite_45 extended CSRNet by adding parallel branches for the last predictive layer. This allowed for uncertainty estimation as well as a way to improve the performance through ensemble averaging. Finally, it is worth mentioning the approach taken in @cite_12 that first estimates the head size and position in order to choose the hyper parameters for the CCNN.
@cite_6 @cite_19 @cite_27 @cite_45 @cite_51 @cite_12 @cite_17
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Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net). Convolutional neural networks (CNNs) have revolutionized medical image analysis over the past few years. The U-Net architecture is one of the most well-known CNN architectures for semantic segmentation and has achieved remarkable successes in many different medical image segmentation applications. The U-Net architecture consists of standard convolution layers, pooling layers, and upsampling layers. These convolution layers learn representative features of input images and construct segmentations based on the features. However, the features learned by standard convolution layers are not distinctive when the differences among different categories are subtle in terms of intensity, location, shape, and size. In this paper, we propose a novel CNN architecture, called Dense-Res-Inception Net (DRINet), which addresses this challenging problem. The proposed DRINet consists of three blocks, namely a convolutional block with dense connections, a deconvolutional block with residual inception modules, and an unpooling block. Our proposed architecture outperforms the U-Net in three different challenging applications, namely multi-class segmentation of cerebrospinal fluid on brain CT images, multi-organ segmentation on abdominal CT images, and multi-class brain tumor segmentation on MR images. How well does a classic deep net architecture like AlexNet or VGG19 classify on a standard dataset such as CIFAR-10 when its "width" --- namely, number of channels in convolutional layers, and number of nodes in fully-connected internal layers --- is allowed to increase to infinity? Such questions have come to the forefront in the quest to theoretically understand deep learning and its mysteries about optimization and generalization. They also connect deep learning to notions such as Gaussian processes and kernels. A recent paper [, 2018] introduced the Neural Tangent Kernel (NTK) which captures the behavior of fully-connected deep nets in the infinite width limit trained by gradient descent; this object was implicit in some other recent papers. A subsequent paper [, 2019] gave heuristic Monte Carlo methods to estimate the NTK and its extension, Convolutional Neural Tangent Kernel (CNTK) and used this to try to understand the limiting behavior on datasets like CIFAR-10. The current paper gives the first efficient exact algorithm (based upon dynamic programming) for computing CNTK as well as an efficient GPU implementation of this algorithm. This results in a significant new benchmark for performance of a pure kernel-based method on CIFAR-10, being 10 higher than the methods reported in [, 2019], and only 5 lower than the performance of the corresponding finite deep net architecture (once batch normalization etc. are turned off). We give the first non-asymptotic proof showing that a fully-trained sufficiently wide net is indeed equivalent to the kernel regression predictor using NTK. Our experiments also demonstrate that earlier Monte Carlo approximation can degrade the performance significantly, thus highlighting the power of our exact kernel computation, which we have applied even to the full CIFAR-10 dataset and 20-layer nets. Recovering images from undersampled linear measurements typically leads to an ill-posed linear inverse problem, that asks for proper statistical priors. Building effective priors is however challenged by the low train and test overhead dictated by real-time tasks; and the need for retrieving visually "plausible" and physically "feasible" images with minimal hallucination. To cope with these challenges, we design a cascaded network architecture that unrolls the proximal gradient iterations by permeating benefits from generative residual networks (ResNet) to modeling the proximal operator. A mixture of pixel-wise and perceptual costs is then deployed to train proximals. The overall architecture resembles back-and-forth projection onto the intersection of feasible and plausible images. Extensive computational experiments are examined for a global task of reconstructing MR images of pediatric patients, and a more local task of superresolving CelebA faces, that are insightful to design efficient architectures. Our observations indicate that for MRI reconstruction, a recurrent ResNet with a single residual block effectively learns the proximal. This simple architecture appears to significantly outperform the alternative deep ResNet architecture by 2dB SNR, and the conventional compressed-sensing MRI by 4dB SNR with 100x faster inference. For image superresolution, our preliminary results indicate that modeling the denoising proximal demands deep ResNets.