Accurate and reliable segmentation of the optic disc in digital fundus images

We describe a complete pipeline for the detection and accurate automatic segmentation of the optic disc in digital fundus images. This procedure provides separation of vascular information and accurate inpainting of vessel-removed images, symmetry-based optic disc localization, and fitting of incrementally complex contour models at increasing resolutions using information related to inpainted images and vessel masks. Validation experiments, performed on a large dataset of images of healthy and pathological eyes, annotated by experts and partially graded with a quality label, demonstrate the good performances of the proposed approach. The method is able to detect the optic disc and trace its contours better than the other systems presented in the literature and tested on the same data. The average error in the obtained contour masks is reasonably close to the interoperator errors and suitable for practical applications. The optic disc segmentation pipeline is currently integrated in a complete software suite for the semiautomatic quantification of retinal vessel properties from fundus camera images (VAMPIRE)

Guided Proofreading of Automatic Segmentations for Connectomics

Automatic cell image segmentation methods in connectomics produce merge and split errors, which require correction through proofreading. Previous research has identified the visual search for these errors as the bottleneck in interactive proofreading. To aid error correction, we develop two classifiers that automatically recommend candidate merges and splits to the user. These classifiers use a convolutional neural network (CNN) that has been trained with errors in automatic segmentations against expert-labeled ground truth. Our classifiers detect potentially-erroneous regions by considering a large context region around a segmentation boundary. Corrections can then be performed by a user with yes/no decisions, which reduces variation of information 7.5x faster than previous proofreading methods. We also present a fully-automatic mode that uses a probability threshold to make merge/split decisions. Extensive experiments using the automatic approach and comparing performance of novice and expert users demonstrate that our method performs favorably against state-of-the-art proofreading methods on different connectomics datasets.Comment: Supplemental material available at http://rhoana.org/guidedproofreading/supplemental.pd

Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines

Many automatically analyzable scientific questions are well-posed and offer a variety of information about the expected outcome a priori. Although often being neglected, this prior knowledge can be systematically exploited to make automated analysis operations sensitive to a desired phenomenon or to evaluate extracted content with respect to this prior knowledge. For instance, the performance of processing operators can be greatly enhanced by a more focused detection strategy and the direct information about the ambiguity inherent in the extracted data. We present a new concept for the estimation and propagation of uncertainty involved in image analysis operators. This allows using simple processing operators that are suitable for analyzing large-scale 3D+t microscopy images without compromising the result quality. On the foundation of fuzzy set theory, we transform available prior knowledge into a mathematical representation and extensively use it enhance the result quality of various processing operators. All presented concepts are illustrated on a typical bioimage analysis pipeline comprised of seed point detection, segmentation, multiview fusion and tracking. Furthermore, the functionality of the proposed approach is validated on a comprehensive simulated 3D+t benchmark data set that mimics embryonic development and on large-scale light-sheet microscopy data of a zebrafish embryo. The general concept introduced in this contribution represents a new approach to efficiently exploit prior knowledge to improve the result quality of image analysis pipelines. Especially, the automated analysis of terabyte-scale microscopy data will benefit from sophisticated and efficient algorithms that enable a quantitative and fast readout. The generality of the concept, however, makes it also applicable to practically any other field with processing strategies that are arranged as linear pipelines.Comment: 39 pages, 12 figure

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

A Critical Review of "Automatic Patch Generation Learned from Human-Written Patches": Essay on the Problem Statement and the Evaluation of Automatic Software Repair

At ICSE'2013, there was the first session ever dedicated to automatic program repair. In this session, Kim et al. presented PAR, a novel template-based approach for fixing Java bugs. We strongly disagree with key points of this paper. Our critical review has two goals. First, we aim at explaining why we disagree with Kim and colleagues and why the reasons behind this disagreement are important for research on automatic software repair in general. Second, we aim at contributing to the field with a clarification of the essential ideas behind automatic software repair. In particular we discuss the main evaluation criteria of automatic software repair: understandability, correctness and completeness. We show that depending on how one sets up the repair scenario, the evaluation goals may be contradictory. Eventually, we discuss the nature of fix acceptability and its relation to the notion of software correctness.Comment: ICSE 2014, India (2014