Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest

Colorectal adenocarcinoma originating in intestinal glandular structures is the most common form of colon cancer. In clinical practice, the morphology of intestinal glands, including architectural appearance and glandular formation, is used by pathologists to inform prognosis and plan the treatment of individual patients. However, achieving good inter-observer as well as intra-observer reproducibility of cancer grading is still a major challenge in modern pathology. An automated approach which quantifies the morphology of glands is a solution to the problem. This paper provides an overview to the Gland Segmentation in Colon Histology Images Challenge Contest (GlaS) held at MICCAI'2015. Details of the challenge, including organization, dataset and evaluation criteria, are presented, along with the method descriptions and evaluation results from the top performing methods

Capsule Networks for Brain Tumor Classification based on MRI Images and Course Tumor Boundaries

According to official statistics, cancer is considered as the second leading cause of human fatalities. Among different types of cancer, brain tumor is seen as one of the deadliest forms due to its aggressive nature, heterogeneous characteristics, and low relative survival rate. Determining the type of brain tumor has significant impact on the treatment choice and patient's survival. Human-centered diagnosis is typically error-prone and unreliable resulting in a recent surge of interest to automatize this process using convolutional neural networks (CNNs). CNNs, however, fail to fully utilize spatial relations, which is particularly harmful for tumor classification, as the relation between the tumor and its surrounding tissue is a critical indicator of the tumor's type. In our recent work, we have incorporated newly developed CapsNets to overcome this shortcoming. CapsNets are, however, highly sensitive to the miscellaneous image background. The paper addresses this gap. The main contribution is to equip CapsNet with access to the tumor surrounding tissues, without distracting it from the main target. A modified CapsNet architecture is, therefore, proposed for brain tumor classification, which takes the tumor coarse boundaries as extra inputs within its pipeline to increase the CapsNet's focus. The proposed approach noticeably outperforms its counterparts

Cross-Classification Clustering: An Efficient Multi-Object Tracking Technique for 3-D Instance Segmentation in Connectomics

Pixel-accurate tracking of objects is a key element in many computer vision applications, often solved by iterated individual object tracking or instance segmentation followed by object matching. Here we introduce cross-classification clustering (3C), a technique that simultaneously tracks complex, interrelated objects in an image stack. The key idea in cross-classification is to efficiently turn a clustering problem into a classification problem by running a logarithmic number of independent classifications per image, letting the cross-labeling of these classifications uniquely classify each pixel to the object labels. We apply the 3C mechanism to achieve state-of-the-art accuracy in connectomics -- the nanoscale mapping of neural tissue from electron microscopy volumes. Our reconstruction system increases scalability by an order of magnitude over existing single-object tracking methods (such as flood-filling networks). This scalability is important for the deployment of connectomics pipelines, since currently the best performing techniques require computing infrastructures that are beyond the reach of most laboratories. Our algorithm may offer benefits in other domains that require pixel-accurate tracking of multiple objects, such as segmentation of videos and medical imagery.Comment: 11 figure

Deep Part Induction from Articulated Object Pairs

Object functionality is often expressed through part articulation -- as when the two rigid parts of a scissor pivot against each other to perform the cutting function. Such articulations are often similar across objects within the same functional category. In this paper, we explore how the observation of different articulation states provides evidence for part structure and motion of 3D objects. Our method takes as input a pair of unsegmented shapes representing two different articulation states of two functionally related objects, and induces their common parts along with their underlying rigid motion. This is a challenging setting, as we assume no prior shape structure, no prior shape category information, no consistent shape orientation, the articulation states may belong to objects of different geometry, plus we allow inputs to be noisy and partial scans, or point clouds lifted from RGB images. Our method learns a neural network architecture with three modules that respectively propose correspondences, estimate 3D deformation flows, and perform segmentation. To achieve optimal performance, our architecture alternates between correspondence, deformation flow, and segmentation prediction iteratively in an ICP-like fashion. Our results demonstrate that our method significantly outperforms state-of-the-art techniques in the task of discovering articulated parts of objects. In addition, our part induction is object-class agnostic and successfully generalizes to new and unseen objects

Gland Instance Segmentation by Deep Multichannel Neural Networks

In this paper, we propose a new image instance segmentation method that segments individual glands (instances) in colon histology images. This is a task called instance segmentation that has recently become increasingly important. The problem is challenging since not only do the glands need to be segmented from the complex background, they are also required to be individually identified. Here we leverage the idea of image-to-image prediction in recent deep learning by building a framework that automatically exploits and fuses complex multichannel information, regional, location and boundary patterns in gland histology images. Our proposed system, deep multichannel framework, alleviates heavy feature design due to the use of convolutional neural networks and is able to meet multifarious requirement by altering channels. Compared to methods reported in the 2015 MICCAI Gland Segmentation Challenge and other currently prevalent methods of instance segmentation, we observe state-of-the-art results based on a number of evaluation metrics

A Brief Survey and an Application of Semantic Image Segmentation for Autonomous Driving

Deep learning is a fast-growing machine learning approach to perceive and understand large amounts of data. In this paper, general information about the deep learning approach which is attracted much attention in the field of machine learning is given in recent years and an application about semantic image segmentation is carried out in order to help autonomous driving of autonomous vehicles. This application is implemented with Fully Convolutional Network (FCN) architectures obtained by modifying the Convolutional Neural Network (CNN) architectures based on deep learning. Experimental studies for the application are utilized 4 different FCN architectures named FCN-AlexNet,FCN-8s, FCN-16s and FCN-32s. For the experimental studies, FCNs are first trained separately and validation accuracies of these trained network models on the used dataset is compared. In addition, image segmentation inferences are visualized to take account of how precisely FCN architectures can segment objects.Comment: A chapter for Springer Book: Handbook of Deep Learning Applications, 2018,[ Pijush Samui, Editor]. (be published

A Comparative Study of Fruit Detection and Counting Methods for Yield Mapping in Apple Orchards

We present new methods for apple detection and counting based on recent deep learning approaches and compare them with state-of-the-art results based on classical methods. Our goal is to quantify performance improvements by neural network-based methods compared to methods based on classical approaches. Additionally, we introduce a complete system for counting apples in an entire row. This task is challenging as it requires tracking fruits in images from both sides of the row. We evaluate the performances of three fruit detection methods and two fruit counting methods on six datasets. Results indicate that the classical detection approach still outperforms the deep learning based methods in the majority of the datasets. For fruit counting though, the deep learning based approach performs better for all of the datasets. Combining the classical detection method together with the neural network based counting approach, we achieve remarkable yield accuracies ranging from 95.56% to 97.83%.Comment: 28 page

X-View: Graph-Based Semantic Multi-View Localization

Global registration of multi-view robot data is a challenging task. Appearance-based global localization approaches often fail under drastic view-point changes, as representations have limited view-point invariance. This work is based on the idea that human-made environments contain rich semantics which can be used to disambiguate global localization. Here, we present X-View, a Multi-View Semantic Global Localization system. X-View leverages semantic graph descriptor matching for global localization, enabling localization under drastically different view-points. While the approach is general in terms of the semantic input data, we present and evaluate an implementation on visual data. We demonstrate the system in experiments on the publicly available SYNTHIA dataset, on a realistic urban dataset recorded with a simulator, and on real-world StreetView data. Our findings show that X-View is able to globally localize aerial-to-ground, and ground-to-ground robot data of drastically different view-points. Our approach achieves an accuracy of up to 85 % on global localizations in the multi-view case, while the benchmarked baseline appearance-based methods reach up to 75 %

Methods for Segmentation and Classification of Digital Microscopy Tissue Images

High-resolution microscopy images of tissue specimens provide detailed information about the morphology of normal and diseased tissue. Image analysis of tissue morphology can help cancer researchers develop a better understanding of cancer biology. Segmentation of nuclei and classification of tissue images are two common tasks in tissue image analysis. Development of accurate and efficient algorithms for these tasks is a challenging problem because of the complexity of tissue morphology and tumor heterogeneity. In this paper we present two computer algorithms; one designed for segmentation of nuclei and the other for classification of whole slide tissue images. The segmentation algorithm implements a multiscale deep residual aggregation network to accurately segment nuclear material and then separate clumped nuclei into individual nuclei. The classification algorithm initially carries out patch-level classification via a deep learning method, then patch-level statistical and morphological features are used as input to a random forest regression model for whole slide image classification. The segmentation and classification algorithms were evaluated in the MICCAI 2017 Digital Pathology challenge. The segmentation algorithm achieved an accuracy score of 0.78. The classification algorithm achieved an accuracy score of 0.81

Convex Shape Prior for Deep Neural Convolution Network based Eye Fundus Images Segmentation

Convex Shapes (CS) are common priors for optic disc and cup segmentation in eye fundus images. It is important to design proper techniques to represent convex shapes. So far, it is still a problem to guarantee that the output objects from a Deep Neural Convolution Networks (DCNN) are convex shapes. In this work, we propose a technique which can be easily integrated into the commonly used DCNNs for image segmentation and guarantee that outputs are convex shapes. This method is flexible and it can handle multiple objects and allow some of the objects to be convex. Our method is based on the dual representation of the sigmoid activation function in DCNNs. In the dual space, the convex shape prior can be guaranteed by a simple quadratic constraint on a binary representation of the shapes. Moreover, our method can also integrate spatial regularization and some other shape prior using a soft thresholding dynamics (STD) method. The regularization can make the boundary curves of the segmentation objects to be simultaneously smooth and convex. We design a very stable active set projection algorithm to numerically solve our model. This algorithm can form a new plug-and-play DCNN layer called CS-STD whose outputs must be a nearly binary segmentation of convex objects. In the CS-STD block, the convexity information can be propagated to guide the DCNN in both forward and backward propagation during training and prediction process. As an application example, we apply the convexity prior layer to the retinal fundus images segmentation by taking the popular DeepLabV3+ as a backbone network. Experimental results on several public datasets show that our method is efficient and outperforms the classical DCNN segmentation methods