A large annotated medical image dataset for the development and evaluation of segmentation algorithms

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community

How to collect high quality segmentations: use human or computer drawn object boundaries?

High quality segmentations must be captured consistently for applications such as biomedical image analysis. While human drawn segmentations are often collected because they provide a consistent level of quality, computer drawn segmentations can be collected efficiently and inexpensively. In this paper, we examine how to leverage available human and computer resources to consistently create high quality segmentations. We propose a quality control methodology. We demonstrate how to apply this approach using crowdsourced and domain expert votes for the "best" segmentation from a collection of human and computer drawn segmentations for 70 objects from a public dataset and 274 objects from biomedical images. We publicly share the library of biomedical images which includes 1,879 manual annotations of the boundaries of 274 objects. We found for the 344 objects that no single segmentation source was preferred and that human annotations are not always preferred over computer annotations. These results motivated us to examine the traditional approach to evaluate segmentation algorithms, which involves comparing the segmentations produced by the algorithms to manual annotations on benchmark datasets. We found that algorithm benchmarking results change when the comparison is made to consensus-voted segmentations. Our results led us to suggest a new segmentation approach that uses machine learning to predict the optimal segmentation source and a modified segmentation evaluation approach.National Science Foundation (IIS-0910908

DroTrack: High-speed Drone-based Object Tracking Under Uncertainty

We present DroTrack, a high-speed visual single-object tracking framework for drone-captured video sequences. Most of the existing object tracking methods are designed to tackle well-known challenges, such as occlusion and cluttered backgrounds. The complex motion of drones, i.e., multiple degrees of freedom in three-dimensional space, causes high uncertainty. The uncertainty problem leads to inaccurate location predictions and fuzziness in scale estimations. DroTrack solves such issues by discovering the dependency between object representation and motion geometry. We implement an effective object segmentation based on Fuzzy C Means (FCM). We incorporate the spatial information into the membership function to cluster the most discriminative segments. We then enhance the object segmentation by using a pre-trained Convolution Neural Network (CNN) model. DroTrack also leverages the geometrical angular motion to estimate a reliable object scale. We discuss the experimental results and performance evaluation using two datasets of 51,462 drone-captured frames. The combination of the FCM segmentation and the angular scaling increased DroTrack precision by up to $9\%$ and decreased the centre location error by $162$ pixels on average. DroTrack outperforms all the high-speed trackers and achieves comparable results in comparison to deep learning trackers. DroTrack offers high frame rates up to 1000 frame per second (fps) with the best location precision, more than a set of state-of-the-art real-time trackers.Comment: 10 pages, 12 figures, FUZZ-IEEE 202

Evaluation of state-of-the-art segmentation algorithms for left ventricle infarct from late Gadolinium enhancement MR images

Studies have demonstrated the feasibility of late Gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) imaging for guiding the management of patients with sequelae to myocardial infarction, such as ventricular tachycardia and heart failure. Clinical implementation of these developments necessitates a reproducible and reliable segmentation of the infarcted regions. It is challenging to compare new algorithms for infarct segmentation in the left ventricle (LV) with existing algorithms. Benchmarking datasets with evaluation strategies are much needed to facilitate comparison. This manuscript presents a benchmarking evaluation framework for future algorithms that segment infarct from LGE CMR of the LV. The image database consists of 30 LGE CMR images of both humans and pigs that were acquired from two separate imaging centres. A consensus ground truth was obtained for all data using maximum likelihood estimation. Six widely-used fixed-thresholding methods and five recently developed algorithms are tested on the benchmarking framework. Results demonstrate that the algorithms have better overlap with the consensus ground truth than most of the n-SD fixed-thresholding methods, with the exception of the FullWidth-at-Half-Maximum (FWHM) fixed-thresholding method. Some of the pitfalls of fixed thresholding methods are demonstrated in this work. The benchmarking evaluation framework, which is a contribution of this work, can be used to test and benchmark future algorithms that detect and quantify infarct in LGE CMR images of the LV. The datasets, ground truth and evaluation code have been made publicly available through the website: https://www.cardiacatlas.org/web/guest/challenges