Rapid automated tracing and feature extraction from retinal fundus images using direct exploratory algorithms

Tracking the optic nervehead in OCT video using dual eigenspaces and an adaptive vascular distribution model

Optical coherence tomography (OCT) is a new ophthalmic imaging modality generating cross sectional views of the retina. OCT systems are essentially Michelson interferometers that form images in 1.5 s by directing a superluminescent diode (SLD) beam over the retinal surface. Involuntary eye motions frequently cause incorrect locations to be imaged. This motion may leave no obvious artifacts in the scan data and can easily go undetected. For glaucoma monitoring especially, knowing the measurement path, typically a circle concentric with the nerve head, is crucial. The commercially available OCT system displays a near-infrared video of the retina showing the SLD beam. This paper presents a prototype system to detect the nerve head and SLD beam in the video, and report the true scan path relative to the nerve head. Low image contrast and limited resolution make the reliable detection of retinal features difficult. In an adaptive model construction phase, the system directly detects retinal vasculature and the nerve head and incrementally builds a model of the current subject's vascular pattern relative to the optic disk. The nerve head identification is multitiered, using a novel dual eigenspace technique and a geometric comparison of detected vessel positions and nerve head hypotheses. In its operational phase, a correspondence is achieved between the currently detected vasculature and the model. Using subjects not included in training, the system located the optic nerve head to within 5 pixels (0.07 optic disk diameters, an error well below clinical significance) in 99.75% of 2800 video fields. In current clinical practice, motions as large as 1-2 disc diameters may go undetected, so this is a vast improvement.

The dual-bootstrap iterative closest point algorithm with application to retinal image registration

Motivated by the problem of retinal image registration, this paper introduces and analyzes a new registration algorithm called Dual-Bootstrap Iterative Closest Point (Dual-Bootstrap ICP). The approach is to start from one or more initial, low-order estimates that are only accurate in small image regions, called bootstrap regions. In each bootstrap region, the algorithm iteratively: 1) refines the transformation estimate using constraints only from within the bootstrap region; 2) expands the bootstrap region; and 3) tests to see if a higher order transformation model can be used, stopping when the region expands to cover the overlap between images. Steps 1): and 3), the bootstrap steps, are governed by the covariance matrix of the estimated transformation. Estimation refinement [Step 2)] uses a novel robust version of the ICP algorithm. In registering retinal image pairs, Dual-Bootstrap ICP is initialized by automatically matching individual vascular landmarks, and it aligns images based on detected blood vessel centerlines. The resulting quadratic transformations are accurate to less than a pixel. On tests involving approximately 6000 image pairs, it successfully registered 99.5% of the pairs containing at least one common landmark, and 100% of the pairs containing at least one common landmark and at least 35% image overlap.

Automated tracing and change analysis of angiogenic vasculature from in vivo multiphoton confocal image time series

Automated methods are described for tracing and analysis of changes in angiogenic vasculature imaged by a multiphoton laser-scanning confocal microscope. Utilizing chronic animal window models, time series of in vivo 3-D images were acquired on approximately the same target volume of the same specimen while undergoing angiogenic change (typically every 24 h for 7 days). Objective, precise, 3-D, rapid, and fully automated vessel morphometry was performed using an adaptive tracing algorithm that is based on a generalized irregular cylinder model of the vasculature. This algorithm was found to be not only adaptive enough for tracing angiogenic vasculature, but also very efficient in its use of computer memory, and fast, taking less than 1 min to trace a 768 x 512 x 32, 8-bit/pixel 3-D image stack on a Dell Pentium III 1-GHz computer. The automatically traced centerlines were manually validated on six image stacks and the average spatial error was measured to be 2 pixels, with an average concordance of 81% between manual and automated traces on a voxel basis. The tracing output includes geometrical statistics of traced vasculature and serves as the basis of statistical change analysis. The computer methods described here are designed to be scalable to much larger hypothesis testing studies involving quantitative measurements of tumor angiogenesis, gene expression relative to known vascular structures, and impact of drug delivery.

A View-Based Approach to Registration: Theory and Application to Vascular Image Registration

This paper presents an approach to registration centered on the notion of a view--a combination of an image resolution, a transformation model, an image region over which the model currently applies, and a set of image primitives from this region. The registration process is divided into three stages: initialization, automatic view generation, and estimation. For a given initial estimate, the latter two alternate until convergence; several initial estimates may be explored. The estimation process uses a novel generalization of the Iterative Closest Point (ICP) technique that simultaneously considers multiple correspondences for each point. View-based registration is applied successfully to alignment of vascular and neuronal images in 2-d and 3-d using similarity, affine, and quadratic transformations.

Rapid automated three-dimensional tracing of neurons from confocal image stacks

Algorithms are presented for fully automatic three-dimensional (3-D) tracing of neurons that are imaged by fluorescence confocal microscopy. Unlike previous voxel-based skeletonization methods, the present approach works by recursively following the neuronal topology, using a set of 4 x N2 directional kernels (e.g., N = 32), guided by a generalized 3-D cylinder model. This method extends our prior work on exploratory tracing of retinal vasculature to 3-D space. Since the centerlines are of primary interest, the 3-D extension can be accomplished by four rather than six sets of kernels. Additional modifications, such as dynamic adaptation of the correlation kernels, and adaptive step size estimation, were introduced for achieving robustness to photon noise, varying contrast, and apparent discontinuity and/or hollowness of structures. The end product is a labeling of all somas present, graph-theoretic representations of all dendritic/axonal structures, and image statistics such as soma volume and centroid, soma interconnectivity, the longest branch, and lengths of all graph branches originating from a soma. This method is able to work directly with unprocessed confocal images, without expensive deconvolution or other preprocessing. It is much faster that skeletonization, typically consuming less than a minute to trace a 70-MB image on a 500-MHz computer. These properties make it attractive for large-scale automated tissue studies that require rapid on-line image analysis, such as high-throughput neurobiology/angiogenesis assays, and initiatives such as the Human Brain Project.

Detection and measurement of retinal vessels in fundus images using amplitude modified second-order Gaussian filter

In this paper, the fitness of estimating vessel profiles with Gaussian function is evaluated and an amplitude-modified second-order Gaussian filter is proposed for the detection and measurement of vessels. Mathematical analysis is given and supported by a simulation and experiments to demonstrate that the vessel width can be measured in linear relationship with the "spreading factor" of the matched filter when the magnitude coefficient of the filter is suitably assigned. The absolute value of vessel diameter can be determined simply by using a precalibrated line, which is typically required since images are always system dependent. The experiment shows that the inclusion of the width measurement in the detection process can improve the performance of matched filter and result in a significant increase in success rate of detection.

Progress towards automated diabetic ocular screening: a review of image analysis and intelligent systems for diabetic retinopathy

Patients with diabetes require annual screening for effective timing of sight-saving treatment. However, the lack of screening and the shortage of ophthalmologists limit the ocular health care available. This is stimulating research into automated analysis of the reflectance images of the ocular fundus. Publications applicable to the automated screening of diabetic retinopathy are summarised. The review has been structured to mimic some of the processes that an ophthalmologist performs when examining the retina. Thus image processing tasks, such as vessel and lesion location, are reviewed before any intelligent or automated systems. Most research has been undertaken in identification of the retinal vasculature and analysis of early pathological changes. Progress has been made in the identification of the retinal vasculature and the more common pathological features, such as small aneurysms and exudates. Ancillary research into image preprocessing has also been identified. In summary, the advent of digital data sets has made image analysis more accessible, although questions regarding the assessment of individual algorithms and whole systems are only just being addressed.

Optimal scheduling of tracing computations for real-time vascular landmark extraction from retinal fundus images

Recently, this group published fast algorithms for automatic tracing (vectorization) of the vasculature in live retinal angiograms, and for the extraction of visual landmarks formed by vascular bifurcations and crossings. These landmarks are used for feature-based image matching for controlling a computer-assisted laser retinal surgery instrument currently under development. This paper describes methods to schedule the vascular tracing computations to maximize the rate of growth of quality of the partial tracing results within a frame cycle. There are two main advantages. First, progressive image matching from partially extracted landmark sets can be faster, and provide an earlier indication of matching failure. Second, the likelihood of successful image matching is greatly improved since the extracted landmarks are of the highest quality for the given computational budget. The scheduling method is based on quantitative measures for the computational work and the quality of landmarks. A coarse grid-based analysis of the image is used to generate seed points for the tracing computations, along with estimates of local edge strengths, orientations, and vessel thickness. These estimates are used to define criteria for real-time preemptive scheduling of the tracing computations. It is shown that the optimal schedule can only be achieved in perfect hindsight, and is thus unrealizable. This leads to scheduling heuristics that approximate the behavior of the optimal algorithm. One such approximation produced approximately 400% improvement in the quality of the partial results at a defined milestone, as compared to random scheduling. The resulting algorithm can be readily implemented on conventional and multiple-processor systems, and is being applied to computer-assisted laser retinal surgery.