1. Articles from Meindert Niemeijer

    1-18 of 18
    1. Multimodal Segmentation of Optic Disc and Cup from SD-OCT and Color Fundus Photographs Using a Machine-Learning Graph-Based Approach

      Multimodal Segmentation of Optic Disc and Cup from SD-OCT and Color Fundus Photographs Using a Machine-Learning Graph-Based Approach

      In this work, a multimodal approach is proposed to use the complementary information from fundus photographs and spectral domain optical coherence tomography ( SD - OCT ) volumes in order to segment the optic disc and cup boundaries. The problem is formulated as an optimization problem where the optimal solution is obtained using a machine-learning theoretical graph-based method. In particular, first the fundus photograph is registered to the 2D projection of the SD - OCT volume. Three inregion cost functions are designed using a random forest classifier corresponding to three regions of cup , rim, and background. Next, the volumes are resampled to create radial ...

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    2. Reproducibility of Diabetic Macular Edema estimates from SD-OCT is affected by the choice of image analysis algorithm

      Reproducibility of Diabetic Macular Edema estimates from SD-OCT is affected by the choice of image analysis algorithm

      Purpose: To evaluate the inter-session repeatability of retinal thickness measurements in patients with diabetic macular edema (DME) using the Heidelberg Spectralis OCT algorithm and a publicly available, 3D graph search based multilayer OCT segmentation algorithm, the Iowa Reference Algorithm. Methods: 30 eyes from 21 patients diagnosed with clinically significant DME were included and underwent consecutive, registered macula-centered spectral domain optical coherence scans (Heidelberg Spectralis). The OCT scans were segmented into separate surfaces and the average thickness between internal limiting membrane and outer retinal pigment epithelium complex surfaces was determined using the Iowa Reference Algorithm. Variability between paired scans was analyzed ...

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    3. Multimodal segmentation of optic disc and cup from stereo fundus and SD-OCT images

      Multimodal segmentation of optic disc and cup from stereo fundus and SD-OCT images

      Glaucoma is one of the major causes of blindness worldwide. One important structural parameter for the diagnosis and management of glaucoma is the cup-to-disc ratio (CDR), which tends to become larger as glaucoma progresses. While approaches exist for segmenting the optic disc and cup within fundus photographs, and more recently, within spectral-domain optical coherence tomography (SD-OCT) volumes, no approaches have been reported for the simultaneous segmentation of these structures within both modalities combined. In this work, a multimodal pixel-classification approach for the segmentation of the optic disc and cup within fundus photographs and SD-OCT volumes is presented. In particular, after ...

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    4. Extending the XNAT archive tool for image and analysis management in ophthalmology research

      Extending the XNAT archive tool for image and analysis management in ophthalmology research

      In ophthalmology, various modalities and tests are utilized to obtain vital information on the eye’s structure and function. For example, optical coherence tomography (OCT) is utilized to diagnose, screen, and aid treatment of eye diseases like macular degeneration or glaucoma. Such data are complemented by photographic retinal fundus images and functional tests on the visual field. DICOM isn’t widely used yet, though, and frequently images are encoded in proprietary formats. The eXtensible Neuroimaging Archive Tool (XNAT) is an open-source NIH-funded framework for research PACS and is in use at the University of Iowa for neurological research applications. Its ...

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    5. Three-dimensional segmentation of fluid-associated abnormalities in retinal OCT: probability constrained graph-search-graph-cut.

      Three-dimensional segmentation of fluid-associated abnormalities in retinal OCT: probability constrained graph-search-graph-cut.

      An automated method is reported for segmenting 3-D fluid-associated abnormalities in the retina, so-called symptomatic exudate-associated derangements (SEAD), from 3-D OCT retinal images of subjects suffering from exudative age-related macular degeneration. In the first stage of a two-stage approach, retinal layers are segmented, candidate SEAD regions identified, and the retinal OCT image is flattened using a candidate-SEAD aware approach. In the second stage, a probability constrained combined graph search-graph cut method refines the candidate SEADs by integrating the candidate volumes into the graph cut cost function as probability constraints. The proposed method was evaluated on 15 spectral domain OCT images ...

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    6. Quantification of External Limiting Membrane Disruption Caused by Diabetic Macular Edema from SD-OCT

      Quantification of External Limiting Membrane Disruption Caused by Diabetic Macular Edema from SD-OCT

      Purpose. Disruption of external limiting membrane (ELM) integrity on spectral-domain optical coherence tomography (SD-OCT) is associated with lower visual acuity outcomes in patients suffering from diabetic macular edema (DME). However, no automated methods to detect ELM and/or determine its integrity from SD-OCT exist. Methods. Sixteen subjects diagnosed with clinically significant DME (CSME) were included and underwent macula-centered SD-OCT (512 × 19 × 496 voxels). Sixteen subjects without retinal thickening and normal acuity were also scanned (200 × 200 × 1024 voxels). Automated quantification of ELM disruption was achieved as follows. First, 11 surfaces were automatically segmented using our standard 3-D graph-search approach, and ...

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    7. Automated segmentation of the choroid from clinical SD-OCT

      Automated segmentation of the choroid from clinical SD-OCT

      Purpose: To develop and evaluate a fully automated three-dimensional method for segmentation of the choroidal vessels, quantification of choroidal vasculature thickness and choriocapillaris-equivalent thickness of the macula, and evaluate repeat variability in normal subjects using standard clinically available SD-OCT. Methods: normal subjects (24) were imaged twice, using clinically available, 3D spectral-domain optical coherence tomography (Cirrus, Carl-Zeiss, Dublin, CA). A novel, fully-automated three-dimensional method was used to segment and visualize the choroidal vasculature in macular scans. Local choroidal vasculature and choriocapillaris-equivalent thicknesses were determined. Reproducibility on repeat imaging was analyzed using overlapping rates, Dice coefficient, and Root Mean Square Coefficient of ...

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    8. Multimodal Retinal Vessel Segmentation from Spectral-Domain Optical Coherence Tomography and Fundus Photography

      Multimodal Retinal Vessel Segmentation from Spectral-Domain Optical Coherence Tomography and Fundus Photography

      Segmenting retinal vessels in optic nerve head (ONH) centered spectral-domain optical coherence tomography (SD-OCT) volumes is particularly challenging due to the projected neural canal opening (NCO) and relatively low visibility in the ONH center. Color fundus photographs provide a relatively high vessel contrast in the region inside the NCO, but have not been previously used to aid the SD-OCT vessel segmentation process. Thus, in this paper, we present two approaches for the segmentation of retinal vessels in SD-OCT volumes that each take advantage of complimentary information from fundus photographs. In the first approach (referred to as the registeredfundus vessel segmentation ...

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    9. Distribution of Damage to the Entire Retinal Ganglion Cell PathwayQuantified Using Spectral-Domain Optical Coherence Tomography Analysis in Patients With Glaucoma

      Distribution of Damage to the Entire Retinal Ganglion Cell PathwayQuantified Using Spectral-Domain Optical Coherence Tomography Analysis in Patients With Glaucoma

      Objectives To test the hypothesis that the amount and distribution of glaucomatous damage along the entire retinal ganglion cell–axonal complex (RGC-AC) can be quantified and to map the RGC-AC connectivity in early glaucoma using automated image analysis of standard spectral-domain optical coherence tomography. Methods Spectral-domain optical coherence tomography volumes were obtained from 116 eyes in 58 consecutive patients with glaucoma or suspected glaucoma. Layer and optic nerve head (ONH) analysis was performed; the mean regional retinal ganglion cell layer thickness (68 regions), nerve fiber layer (NFL) thickness (120 regions), and ONH rim area (12 wedge-shaped regions) were determined. Maps ...

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    10. Registration of 3D spectral OCT volumes combining ICP with a graph-based approach

      Registration of 3D spectral OCT volumes combining ICP with a graph-based approach

      The introduction of spectral Optical Coherence Tomography (OCT) scanners has enabled acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D-OCT is used to detect and manage eye diseases such as glaucoma and age-related macular degeneration. To follow-up patients over time, image registration is a vital tool to enable more precise, quantitative comparison of disease states. In this work we present a 3D registrationmethod based on a two-step approach. In the first step we register both scans in the XY domain using an Iterative Closest Point (ICP) based algorithm. This algorithm is applied to vessel segmentations obtained from ...

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    11. 2-D Pattern of Nerve Fiber Bundles in Glaucoma Emerging from Spectral-Domain Optical Coherence Tomography

      2-D Pattern of Nerve Fiber Bundles in Glaucoma Emerging from Spectral-Domain Optical Coherence Tomography
      Purpose: To correlate the thicknesses of focal regions of the macular ganglion cell layer with those of the peripapillary nerve fiber layer using spectral-domain optical coherence tomography (SD-OCT) in glaucoma subjects. Methods: Macula and optic-nerve-head SD-OCT volumes were obtained in 57 eyes of 57 subjects with open-angle glaucoma or glaucoma suspicion. Using a custom automated computer algorithm, the thickness of 66 macular ganglion cell layer regions and the thickness of 12 peripapillary nerve fiber layer regions were measured from registered SD-OCT volumes. The mean thickness of each ganglion-cell-layer region was correlated to the mean thickness of each peripapillary-nerve-fiber-layer region across ...
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    12. Automated multimodality concurrent classification for segmenting vessels in 3D spectral OCT and color fundus images

      Automated multimodality concurrent classification for segmenting vessels in 3D spectral OCT and color fundus images

      Segmenting vessels in spectral-domain optical coherence tomography (SD-OCT) volumes is particularly challenging in the region near and inside the neural canal opening (NCO). Furthermore, accurately segmenting them in color fundus photographs also presents a challenge near the projected NCO. However, both modalities also provide complementary information to help indicate vessels, such as a better NCO contrast from the NCO-aimed OCT projection image and a better vessel contrast inside the NCO from fundus photographs. We thus present a novel multimodal automated classification approach for simultaneously segmenting vessels in SD-OCT volumes and fundus photographs, with a particular focus on better segmenting vessels ...

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    13. Automated Segmentation of 3-D Spectral OCT Retinal Blood Vessels by Neural Canal Opening False Positive Suppression

      Automated Segmentation of 3-D Spectral OCT Retinal Blood Vessels by Neural Canal Opening False Positive Suppression

      We present a method for automatically segmenting the blood vessels in optic nerve head (ONH) centered spectral-domain optical coherence tomography (SD-OCT) volumes, with a focus on the ability to segment the vessels in the region near the neural canal opening (NCO). The algorithm first pre-segments the NCO using a graph-theoretic approach. Oriented Gabor wavelets rotated around the center of the NCO are applied to extract features in a 2-D vessel-aimed projection image. Corresponding oriented NCO-based templates are utilized to help suppress the false positive tendency near the NCO boundary. The vessels are identified in a vessel-aimed projection image using a ...

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    14. 3-D segmentation of retinal blood vessels in spectral-domain OCT volumes of the optic nerve head

      3-D segmentation of retinal blood vessels in spectral-domain OCT volumes of the optic nerve head

      Segmentation of retinal blood vessels can provide important information for detecting and tracking retinal vascular diseases including diabetic retinopathy, arterial hypertension, arteriosclerosis and retinopathy of prematurity (ROP). Many studies on 2-D segmentation of retinal blood vessels from a variety of medical images have been performed. However, 3-D segmentation of retinal blood vessels from spectral-domain optical coherence tomography (OCT) volumes, which is capable of providing geometrically accurate vessel models, to the best of our knowledge, has not been previously studied. The purpose of this study is to develop and evaluate a method that can automatically detect 3-D retinal blood vessels from ...

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    15. Automated Segmentation of the Cup and Rim from Spectral Domain OCT of the Optic Nerve Head

      Purpose: to evaluate the performance of an automated algorithm for determination of the cup and rim from close-to-isotropic spectral domain (SD) OCT images of the optic nerve head (ONH) and compare to the cup and rim as determined by glaucoma experts from stereo color photographs of the same eye. Methods: 34 consecutive patients with glaucoma were included in the study, and the ONH in their left eye was imaged with SD-OCT (Zeiss Cirrus) and stereo color photography (Nidek 3Dx) on the same day. Cup and rim were segmented in all ONH OCT volumes by a novel voxel column classification algorithm ...
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    16. 3-D segmentation of the rim and cup in spectral-domain optical coherence tomography volumes of the optic nerve head

      3-D segmentation of the rim and cup in spectral-domain optical coherence tomography volumes of the optic nerve head

      Glaucoma is a group of diseases which can cause vision loss and blindness due to gradual damage to the optic nerve. The ratio of the optic disc cup to the optic disc is an important structural indicator for assessing the presence of glaucoma. The purpose of this study is to develop and evaluate a method which can segment the optic disc cup and neuroretinal rim in spectral-domain OCT scans centered on the optic nerve head. Our method starts by segmenting 3 intraretinal surfaces using a fast multiscale 3-D graph search method. Based on one of the segmented surfaces, the retina ...

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    17. Automated segmentation of the optic disc margin in 3-D optical coherence tomography images using a graph-theoretic approach

      Automated segmentation of the optic disc margin in 3-D optical coherence tomography images using a graph-theoretic approach

      The optic disc margin is of interest due to its use for detecting and managing glaucoma. We developed a method for segmenting the optic disc margin of the optic nerve head (ONH) in spectral-domain optical coherence tomography (OCT) images using a graph-theoretic approach. A small number of slices surrounding the Bruch's membrane opening (BMO) plane was taken and used for creating planar 2-D projection images. An edge-based cost function - more specifically, a signed edge-based term favoring a dark-to-bright transition in the vertical direction of polar projection images (corresponding to the radial direction in Cartesian coordinates) - was obtained. Information from ...

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    18. Vessel segmentation in 3D spectral OCT scans of the retina

      Vessel segmentation in 3D spectral OCT scans of the retina

      The latest generation of spectral optical coherence tomography (OCT) scanners is able to image 3D cross-sectional volumes of the retina at a high resolution and high speed. These scans offer a detailed view of the structure of the retina. Automated segmentation of the vessels in these volumes may lead to more objective diagnosis of retinal vascular disease including hypertensive retinopathy, retinopathy of prematurity. Additionally, vessel segmentation can allow color fundus images to be registered to these 3D volumes, possibly leading to a better understanding of the structure and localization of retinal structures and lesions. In this paper we present a ...

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    1-18 of 18
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    1. (18 articles) University of Iowa
    2. (18 articles) Michael D. Abràmoff
    3. (15 articles) Kyungmoo Lee
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    Vessel segmentation in 3D spectral OCT scans of the retina 3-D segmentation of the rim and cup in spectral-domain optical coherence tomography volumes of the optic nerve head Automated segmentation of the optic disc margin in 3-D optical coherence tomography images using a graph-theoretic approach 3-D segmentation of retinal blood vessels in spectral-domain OCT volumes of the optic nerve head Automated Segmentation of 3-D Spectral OCT Retinal Blood Vessels by Neural Canal Opening False Positive Suppression Automated multimodality concurrent classification for segmenting vessels in 3D spectral OCT and color fundus images Registration of 3D spectral OCT volumes combining ICP with a graph-based approach Distribution of Damage to the Entire Retinal Ganglion Cell PathwayQuantified Using Spectral-Domain Optical Coherence Tomography Analysis in Patients With Glaucoma Multimodal Retinal Vessel Segmentation from Spectral-Domain Optical Coherence Tomography and Fundus Photography Special Section Guest Editorial: Advances in Retinal Imaging Optical coherence tomography angiography-derived flow density: a review of the influencing factors Changes in retinal and choriocapillaris density in diabetic patients receiving anti-vascular endothelial growth factor treatment using optical coherence tomography angiography