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Register a new userPlant Stem Segmentation Using Fast Ground Truth Generation
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Added by
Sriram Baireddy
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Accurately phenotyping plant wilting is important for understanding responses to environmental stress. Analysis of the shape of plants can potentially be used to accurately quantify the degree of wilting. Plant shape analysis can be enhanced by locating the stem, which serves as a consistent reference point during wilting. In this paper, we show that deep learning methods can accurately segment tomato plant stems. We also propose a control-point-based ground truth method that drastically reduces the resources needed to create a training dataset for a deep learning approach. Experimental results show the viability of both our proposed ground truth approach and deep learning based stem segmentation.
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A key limitation of deep convolutional neural networks (DCNN) based image segmentation methods is the lack of generalizability. Manually traced training images are typically required when segmenting organs in a new imaging modality or from distinct disease cohort. The manual efforts can be alleviated if the manually traced images in one imaging modality (e.g., MRI) are able to train a segmentation network for another imaging modality (e.g., CT). In this paper, we propose an end-to-end synthetic segmentation network (SynSeg-Net) to train a segmentation network for a target imaging modality without having manual labels. SynSeg-Net is trained by using (1) unpaired intensity images from source and target modalities, and (2) manual labels only from source modality. SynSeg-Net is enabled by the recent advances of cycle generative adversarial networks (CycleGAN) and DCNN. We evaluate the performance of the SynSeg-Net on two experiments: (1) MRI to CT splenomegaly synthetic segmentation for abdominal images, and (2) CT to MRI total intracranial volume synthetic segmentation (TICV) for brain images. The proposed end-to-end approach achieved superior performance to two stage methods. Moreover, the SynSeg-Net achieved comparable performance to the traditional segmentation network using target modality labels in certain scenarios. The source code of SynSeg-Net is publicly available (https://github.com/MASILab/SynSeg-Net).
Deep neural networks have been very successful in image estimation applications such as compressive-sensing and image restoration, as a means to estimate images from partial, blurry, or otherwise degraded measurements. These networks are trained on a large number of corresponding pairs of measurements and ground-truth images, and thus implicitly learn to exploit domain-specific image statistics. But unlike measurement data, it is often expensive or impractical to collect a large training set of ground-truth images in many application settings. In this paper, we introduce an unsupervised framework for training image estimation networks, from a training set that contains only measurements---with two varied measurements per image---but no ground-truth for the full images desired as output. We demonstrate that our framework can be applied for both regular and blind image estimation tasks, where in the latter case parameters of the measurement model (e.g., the blur kernel) are unknown: during inference, and potentially, also during training. We evaluate our method for training networks for compressive-sensing and blind deconvolution, considering both non-blind and blind training for the latter. Our unsupervised framework yields models that are nearly as accurate as those from fully supervised training, despite not having access to any ground-truth images.
Deep convolutional neural networks (CNNs) have shown outstanding performance in the task of semantically segmenting images. However, applying the same methods on 3D data still poses challenges due to the heavy memory requirements and the lack of structured data. Here, we propose LatticeNet, a novel approach for 3D semantic segmentation, which takes as input raw point clouds. A PointNet describes the local geometry which we embed into a sparse permutohedral lattice. The lattice allows for fast convolutions while keeping a low memory footprint. Further, we introduce DeformSlice, a novel learned data-dependent interpolation for projecting lattice features back onto the point cloud. We present results of 3D segmentation on various datasets where our method achieves state-of-the-art performance.
Fast-AT is an automatic thumbnail generation system based on deep neural networks. It is a fully-convolutional deep neural network, which learns specific filters for thumbnails of different sizes and aspect ratios. During inference, the appropriate filter is selected depending on the dimensions of the target thumbnail. Unlike most previous work, Fast-AT does not utilize saliency but addresses the problem directly. In addition, it eliminates the need to conduct region search on the saliency map. The model generalizes to thumbnails of different sizes including those with extreme aspect ratios and can generate thumbnails in real time. A data set of more than 70,000 thumbnail annotations was collected to train Fast-AT. We show competitive results in comparison to existing techniques.
Grapevine winter pruning is a complex task, that requires skilled workers to execute it correctly. The complexity of this task is also the reason why it is time consuming. Considering that this operation takes about 80-120 hours/ha to be completed, and therefore is even more crucial in large-size vineyards, an automated system can help to speed up the process. To this end, this paper presents a novel multidisciplinary approach that tackles this challenging task by performing object segmentation on grapevine images, used to create a representative model of the grapevine plants. Second, a set of potential pruning points is generated from this plant representation. We will describe (a) a methodology for data acquisition and annotation, (b) a neural network fine-tuning for grapevine segmentation, (c) an image processing based method for creating the representative model of grapevines, starting from the inferred segmentation and (d) potential pruning points detection and localization, based on the plant model which is a simplification of the grapevine structure. With this approach, we are able to identify a significant set of potential pruning points on the canes, that can be used, with further selection, to derive the final set of the real pruning points.
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