Vessel tech: a high-accuracy pipeline for comprehensive mouse retinal vasculature characterization.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang X
PROVIDER: S-EPMC7920901 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:While recent advances in deep learning have significantly advanced the state of the art for vessel detection in color fundus (CF) images, the success for detecting vessels in fluorescein angiography (FA) has been stymied due to the lack of labeled ground truth datasets. We propose a novel pipeline to detect retinal vessels in FA images using deep neural networks (DNNs) that reduces the effort required for generating labeled ground truth data by combining two key components: cross-modality transfer and human-in-the-loop learning. The cross-modality transfer exploits concurrently captured CF and fundus FA images. Binary vessels maps are first detected from CF images with a pre-trained neural network and then are geometrically registered with and transferred to FA images via robust parametric chamfer alignment to a preliminary FA vessel detection obtained with an unsupervised technique. Using the transferred vessels as initial ground truth labels for deep learning, the human-in-the-loop approach progressively improves the quality of the ground truth labeling by iterating between deep-learning and labeling. The approach significantly reduces manual labeling effort while increasing engagement. We highlight several important considerations for the proposed methodology and validate the performance on three datasets. Experimental results demonstrate that the proposed pipeline significantly reduces the annotation effort and the resulting deep learning methods outperform prior existing FA vessel detection methods by a significant margin. A new public dataset, RECOVERY-FA19, is introduced that includes high-resolution ultra-widefield images and accurately labeled ground truth binary vessel maps.
| S-EPMC7648732 | biostudies-literature
Project description:We sought to identify differentially expressed genes in several animal models of a retinal disease exhibiting vascular abnormalities and/or angiogenesis compared to control animals. Retinal microvessels were isolated from three models (RD1, Grhl3ct (Curlytail), VLDLR knock-out) and one rat model (RCS dystrophic rat), as well as from C57BL/J6 mice and non-dystrophic RCS rats as controls. Animals were used at ages appropriate to the age of vascular change of each model. Microvessels were isolated from the retinas and RNA was extracted and used in the microarray.
2013-09-13 | E-MEXP-3323 | biostudies-arrayexpress
Project description:Trypsin digest is the gold standard method to analyze the retinal vasculature (1-5). It allows visualization of the entire network of complex three-dimensional retinal blood vessels and capillaries by creating a two-dimensional flat-mount of the interconnected vascular channels after digestion of the non-vascular components of the retina. This allows one to study various pathologic vascular changes, such as microaneurysms, capillary degeneration, and abnormal endothelial to pericyte ratios. However, the method is technically challenging, especially in mice, which have become the most widely available animal model to study the retina because of the ease of genetic manipulations (6,7). In the mouse eye, it is particularly difficult to completely remove the non-vascular components while maintaining the overall architecture of the retinal blood vessels. To date, there is a dearth of literature that describes the trypsin digest technique in detail in the mouse. This manuscript provides a detailed step-by-step methodology of the trypsin digest in mouse retina, while also providing tips on troubleshooting difficult steps.
| S-EPMC3913093 | biostudies-literature
Project description:PurposeTo develop a reliable and simplified method to assess choroid and retinal vasculature on whole mount and cross sections in mice using tomato lectin (TL; Lycopersicon esculentum).MethodsAlbino mice (n = 27) received 1 mg/mL of TL (conjugated to Dylight-594) intravascularly through the tail vein, jugular vein, or cardiac left ventricle. Whole mounts of the retina and choroid were evaluated using fluorescence microscopy. Perfusion with GSL-IB4 conjugated to Dylight-594 and fluorescein isothiocyanate was performed to compare against labeling with TL. Co-labeling of choroidal endothelial cells with perfused TL on cross-sections with antibodies directed against the choriocapillaris-restricted endothelial cell marker CA4 was performed. The percentage of perfused choroidal and retinal vessels was assessed semiquantitatively. One mouse was subjected to thermal laser damage before perfusion to cause retinal and choroidal vasculature ablation.ResultsIntravascular injection of TL led to consistent, robust labeling of retinal and choroidal vascular walls. On cross-sections, choriocapillaris was co-labeled with CA4 and TL. On flat mount, TL perfusion resulted in better labeling of choroidal vessels using tail/jugular vein injection compared with cardiac perfusion (P < .01). More consistent labeling of the choroidal and retinal vascular trees was observed with TL than with GSL-IB4. Vascular damage caused by laser ablation was detected readily using this method.ConclusionsTL injection intravascularly can reliably label normal and ablated choroid and retinal vasculature in mouse in a quick, simple manner.Translational relevanceThese data will help to facilitate modeling in rodents for diseases such as age-related macular degeneration, diabetes, and other ischemic/angiogenic processes that can also be used for treatment evaluation.
| S-EPMC7255627 | biostudies-literature
Project description:PurposeTo investigate whether Epac1 is key to Compound 49b's regulation of zonula occluden 1 (ZO-1) and occludin levels in human retinal endothelial cells (REC) and in an Epac1 vascular-specific conditional knockout mouse retina.MethodsPrimary REC were grown in normal (5 mM) or high glucose (25 mM). Some cells were treated with a novel β-adrenergic receptor agonist, Compound 49b. Additional dishes were treated with Epac1 siRNA or Compound 49b + Epac1 siRNA. Protein levels of ZO-1, occludin, VEGF, and protein kinase C zeta (PKCz) were measured by Western blotting. Cell permeability was measured in REC grown in normal or high glucose and treated with Compound 49b, a specific Epac 1 agonist (8-CPT-2'-O-Me-cAMP), or VEGF. Epac1 floxed and cdh5-Cre mice were bred to generate Epac1 knockout mice in vascular endothelial cells. Immunofluorescence was done on retinal flatmounts from the floxed and Cre-Lox mice for occludin and ZO-1. Western blotting was also done for both proteins in whole retinal lysates from the mice.ResultsHigh glucose significantly reduced ZO-1 and occludin protein levels, which was associated with reduced cell adhesion. Compound 49b increased endothelial cell barrier protein levels through active Epac1. Knockout of Epac1 in vascular endothelial cells substantially reduced ZO-1 and occludin staining in retinal flatmounts, as well as protein levels.ConclusionsCompound 49b increased ZO-1 and occludin protein levels, likely leading to decreased permeability.
| S-EPMC5256679 | biostudies-literature
Project description:In this work, non-invasive high-spatial resolution three-dimensional (3D) X-ray micro-computed tomography (μCT) of healthy mouse lung vasculature is performed. Methodologies are presented for filtering, segmenting, and skeletonizing the collected 3D images. Novel methods for the removal of spurious branch artefacts from the skeletonized 3D image are introduced, and these novel methods involve a combination of distance transform gradients, diameter-length ratios, and the fast marching method (FMM). These new techniques of spurious branch removal result in the consistent removal of spurious branches without compromising the connectivity of the pulmonary circuit. Analysis of the filtered, skeletonized, and segmented 3D images is performed using a newly developed Vessel Network Extraction algorithm to fully characterize the morphology of the mouse pulmonary circuit. The removal of spurious branches from the skeletonized image results in an accurate representation of the pulmonary circuit with significantly less variability in vessel diameter and vessel length in each generation. The branching morphology of a full pulmonary circuit is characterized by the mean diameter per generation and number of vessels per generation. The methods presented in this paper lead to a significant improvement in the characterization of 3D vasculature imaging, allow for automatic separation of arteries and veins, and for the characterization of generations containing capillaries and intrapulmonary arteriovenous anastomoses (IPAVA).
| S-EPMC8594947 | biostudies-literature
Project description:To enhance the use of Whole Genome Sequencing (WGS) in clinical practice, it is still necessary to standardize data analysis pipelines. Herein, we aimed to define a WGS-based algorithm for the accurate interpretation of variants in inherited retinal dystrophies (IRD). This study comprised 429 phenotyped individuals divided into three cohorts. A comparison of 14 pathogenicity predictors, and the re-definition of its cutoffs, were performed using panel-sequencing curated data from 209 genetically diagnosed individuals with IRD (training cohort). The optimal tool combinations, previously validated in 50 additional IRD individuals, were also tested in patients with hereditary cancer (n = 109), and with neurological diseases (n = 47) to evaluate the translational value of this approach (validation cohort). Then, our workflow was applied for the WGS-data analysis of 14 individuals from genetically undiagnosed IRD families (discovery cohort). The statistical analysis showed that the optimal filtering combination included CADDv1.6, MAPP, Grantham, and SIFT tools. Our pipeline allowed the identification of one homozygous variant in the candidate gene CFAP20 (c.337 C > T; p.Arg113Trp), a conserved ciliary gene, which was abundantly expressed in human retina and was located in the photoreceptors layer. Although further studies are needed, we propose CFAP20 as a candidate gene for autosomal recessive retinitis pigmentosa. Moreover, we offer a translational strategy for accurate WGS-data prioritization, which is essential for the advancement of personalized medicine.
| S-EPMC8897414 | biostudies-literature
Project description:BackgroundVision loss due to vascular disease of the retina is a leading cause of blindness in the world. Retinal angiomatous proliferation (RAP) is a subgroup of neovascular age-related macular degeneration (AMD), whereby abnormal blood vessels develop in the retina leading to debilitating vision loss and eventual blindness. The novel mouse strain, neoretinal vascularization 2 (NRV2), shows spontaneous fundus changes associated with abnormal neovascularization. The purpose of this study is to characterize the induction of pathologic angiogenesis in this mouse model.MethodsThe NRV2 mice were examined from postnatal day 12 (p12) to 3 months. The phenotypic changes within the retina were evaluated by fundus photography, fluorescein angiography, optical coherence tomography, and immunohistochemical and electron microscopic analysis. The pathological neovascularization was imaged by confocal microscopy and reconstructed using three-dimensional image analysis software.ResultsWe found that NRV2 mice develop multifocal retinal depigmentation in the posterior fundus. Depigmented lesions developed vascular leakage observed by fluorescein angiography. The spontaneous angiogenesis arose from the retinal vascular plexus at postnatal day (p)15 and extended toward retinal pigment epithelium (RPE). By three months of age, histological analysis revealed encapsulation of the neovascular lesion by the RPE in the photoreceptor cell layer and subretinal space.ConclusionsThe NRV2 mouse strain develops early neovascular lesions within the retina, which grow downward towards the RPE beginning at p15. This retinal neovascularization model mimics early stages of human retinal angiomatous proliferation (RAP) and will likely be a useful in elucidating targeted therapeutics for patients with ocular neovascular disease.
| S-EPMC4154693 | biostudies-literature
Project description:PurposeFamilial exudative vitreoretinopathy (FEVR) is caused by mutations in the genes encoding low-density lipoprotein receptor-related protein (LRP5) or its interacting partners, namely frizzled class receptor 4 (FZD4) and norrin cystine knot growth factor (NDP). Mouse models for Lrp5, Fzd4, and Ndp have proven to be important for understanding the retinal pathophysiology underlying FEVR and systemic abnormalities related to defective Wnt signaling. Here, we report a new mouse mutant, tvrm111B, which was identified by electroretinogram (ERG) screening of mice generated in the Jackson Laboratory Translational Vision Research Models (TVRM) mutagenesis program.MethodsERGs were used to examine outer retinal physiology. The retinal vasculature was examined by in vivo retinal imaging, as well as by histology and immunohistochemistry. The tvrm111B locus was identified by genetic mapping of mice generated in a cross to DBA/2J, and subsequent sequencing analysis. Gene expression was examined by real-time PCR of retinal RNA. Bone mineral density (BMD) was examined by peripheral dual-energy X-ray absorptiometry.ResultsThe tvrm111B allele is inherited as an autosomal recessive trait. Genetic mapping of the decreased ERG b-wave phenotype of tvrm111B mice localized the mutation to a region on chromosome 19 that included Lrp5. Sequencing of Lrp5 identified the insertion of a cytosine (c.4724_4725insC), which is predicted to cause a frameshift that disrupts the last three of five conserved PPPSPxS motifs in the cytoplasmic domain of LRP5, culminating in a premature termination. In addition to a reduced ERG b-wave, Lrp5tvrm111B homozygotes have low BMD and abnormal features of the retinal vasculature that have been reported previously in Lrp5 mutant mice, including persistent hyaloid vessels, leakage on fluorescein angiography, and an absence of the deep retinal capillary bed.ConclusionsThe phenotype of the Lrp5tvrm111B mutant includes abnormalities of the retinal vasculature and of BMD. This model may be a useful resource to further our understanding of the biological role of LRP5 and to evaluate experimental therapies for FEVR or other conditions associated with LRP5 dysfunction.
| S-EPMC5360454 | biostudies-literature
Project description:Purpose: To present a methodology for quantification of the canine retinal vasculature imaged by optical coherence tomography angiography (OCTA) and validate this approach by comparison with fluorescein angiography (FA) and confocal imaging of retinal wholemounts labelled by immunohistochemistry (IHC). Methods: Six normal adult dogs underwent retinal OCTA imaging in both eyes. The images extracted from the different microvascular plexuses at eight retinal locations spanning the central and mid-peripheral fundus were analyzed using the AngioTool software. FA was performed in one eye and was compared to the OCTA images. Six eyes from three dogs were processed by IHC to examine the retinal vasculature. Results: A total of four retinal plexuses were identified by OCTA in the canine retina, and their density and topographical pattern varied with eccentricity. OCTA offered improved resolution over FA with the advantage of allowing imaging of the individual plexuses. Detection by OCTA of small vessels within the deep capillary plexus was possible and approached the level of resolution achieved with ex vivo imaging of the retinal vasculature by confocal microscopy/IHC. The plexuses herein described are analogous to human retinal vasculature. Conclusion: OCTA can be used to image and quantify non-invasively the vascular retinal networks of the canine retina. We provide normative data in eight different retinal locations that can be imaged non-invasively with this technology. This could support analysis of retinal vascular changes associated with disease and following therapeutic intervention.
| S-EPMC8710516 | biostudies-literature