NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

Reconstructive Sparse Code Transfer for Contour Detection and Semantic Labeling

We frame the task of predicting a semantic labeling as a sparse reconstruction procedure that applies a target-specific learned transfer function to a generic deep sparse code representation of an image. This strategy partitions training into two distinct stages. First, in an unsupervised manner, we learn a set of generic dictionaries optimized for sparse coding of image patches. We train a multilayer representation via recursive sparse dictionary learning on pooled codes output by earlier layers. Second, we encode all training images with the generic dictionaries and learn a transfer function that optimizes reconstruction of patches extracted from annotated ground-truth given the sparse codes of their corresponding image patches. At test time, we encode a novel image using the generic dictionaries and then reconstruct using the transfer function. The output reconstruction is a semantic labeling of the test image. Applying this strategy to the task of contour detection, we demonstrate performance competitive with state-of-the-art systems. Unlike almost all prior work, our approach obviates the need for any form of hand-designed features or filters. To illustrate general applicability, we also show initial results on semantic part labeling of human faces. The effectiveness of our approach opens new avenues for research on deep sparse representations. Our classifiers utilize this representation in a novel manner. Rather than acting on nodes in the deepest layer, they attach to nodes along a slice through multiple layers of the network in order to make predictions about local patches. Our flexible combination of a generatively learned sparse representation with discriminatively trained transfer classifiers extends the notion of sparse reconstruction to encompass arbitrary semantic labeling tasks.Comment: to appear in Asian Conference on Computer Vision (ACCV), 201

Machine learning methods for histopathological image analysis

Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.Comment: 23 pages, 4 figure

Annotating Object Instances with a Polygon-RNN

We propose an approach for semi-automatic annotation of object instances. While most current methods treat object segmentation as a pixel-labeling problem, we here cast it as a polygon prediction task, mimicking how most current datasets have been annotated. In particular, our approach takes as input an image crop and sequentially produces vertices of the polygon outlining the object. This allows a human annotator to interfere at any time and correct a vertex if needed, producing as accurate segmentation as desired by the annotator. We show that our approach speeds up the annotation process by a factor of 4.7 across all classes in Cityscapes, while achieving 78.4% agreement in IoU with original ground-truth, matching the typical agreement between human annotators. For cars, our speed-up factor is 7.3 for an agreement of 82.2%. We further show generalization capabilities of our approach to unseen datasets

Crowdsourcing in Computer Vision

Computer vision systems require large amounts of manually annotated data to properly learn challenging visual concepts. Crowdsourcing platforms offer an inexpensive method to capture human knowledge and understanding, for a vast number of visual perception tasks. In this survey, we describe the types of annotations computer vision researchers have collected using crowdsourcing, and how they have ensured that this data is of high quality while annotation effort is minimized. We begin by discussing data collection on both classic (e.g., object recognition) and recent (e.g., visual story-telling) vision tasks. We then summarize key design decisions for creating effective data collection interfaces and workflows, and present strategies for intelligently selecting the most important data instances to annotate. Finally, we conclude with some thoughts on the future of crowdsourcing in computer vision.Comment: A 69-page meta review of the field, Foundations and Trends in Computer Graphics and Vision, 201

Fair comparison of skin detection approaches on publicly available datasets

Skin detection is the process of discriminating skin and non-skin regions in a digital image and it is widely used in several applications ranging from hand gesture analysis to track body parts and face detection. Skin detection is a challenging problem which has drawn extensive attention from the research community, nevertheless a fair comparison among approaches is very difficult due to the lack of a common benchmark and a unified testing protocol. In this work, we investigate the most recent researches in this field and we propose a fair comparison among approaches using several different datasets. The major contributions of this work are an exhaustive literature review of skin color detection approaches, a framework to evaluate and combine different skin detector approaches, whose source code is made freely available for future research, and an extensive experimental comparison among several recent methods which have also been used to define an ensemble that works well in many different problems. Experiments are carried out in 10 different datasets including more than 10000 labelled images: experimental results confirm that the best method here proposed obtains a very good performance with respect to other stand-alone approaches, without requiring ad hoc parameter tuning. A MATLAB version of the framework for testing and of the methods proposed in this paper will be freely available from https://github.com/LorisNann