Madhusudhana Gargesha

Ultrahigh-speed optical coherence tomography imaging and visualization of the embryonic avian heart using a buffered Fourier Domain Mode Locked laser

The embryonic avian heart is an important model for studying cardiac developmental biology. The mechanisms that govern the development of a four-chambered heart from a peristaltic heart tube are largely unknown due in part to a lack of adequate imaging technology. Due to the small size and rapid motion of the living embryonic avian heart, an imaging system with high spatial and temporal resolution is required to study these models. Here, an optical coherence tomography (OCT) system using a buffered Fourier Domain Mode Locked (FDML) laser is applied for ultrahigh-speed non-invasive imaging of embryonic quail hearts at 100,000 axial scans per second. The high scan rate enables the acquisition of high temporal resolution 2D datasets (195 frames per second or 5.12 ms between frames) and 3D datasets (10 volumes per second). Spatio-temporal details of cardiac motion not resolvable using previous OCT technology are analyzed. Visualization and measurement techniques are developed to non-invasively observe and quantify cardiac motion throughout the brief period of systole (less than 50 msec) and diastole. This marks the first time that the preseptated embryonic avian heart has been imaged in 4D without the aid of gating and the first time it has been viewed in cross section during looping with extremely high temporal resolution, enabling the observation of morphological dynamics of the beating heart during systole.

Mouse and human phenotypes indicate a critical conserved role for ERK2 signaling in neural crest development

Disrupted ERK1/2 (MAPK3/MAPK1) MAPK signaling has been associated with several developmental syndromes in humans; however, mutations in ERK1 or ERK2 have not been described. We demonstrate haplo-insufficient ERK2 expression in patients with a novel ≈1 Mb micro-deletion in distal 22q11.2, a region that includes ERK2. These patients exhibit conotruncal and craniofacial anomalies that arise from perturbation of neural crest development and exhibit defects comparable to the DiGeorge syndrome spectrum. Remarkably, these defects are replicated in mice by conditional inactivation of ERK2 in the developing neural crest. Inactivation of upstream elements of the ERK cascade (B-Raf and C-Raf, MEK1 and MEK2) or a downstream effector, the transcription factor serum response factor resulted in analogous developmental defects. Our findings demonstrate that mammalian neural crest development is critically dependent on a RAF/MEK/ERK/serum response factor signaling pathway and suggest that the craniofacial and cardiac outflow tract defects observed in patients with a distal 22q11.2 micro-deletion are explained by deficiencies in neural crest autonomous ERK2 signaling.

High temporal resolution OCT using image-based retrospective gating

High temporal resolution OCT imaging is very advantageous for analyzing cardiac mechanics in the developing embryonic heart of small animals. An image-based retrospective gating technique is presented to increase the effective temporal resolution of an OCT system and to allow visualization of systolic dynamics in 3D. The gating technique employs image similarity measures for rearranging asynchronously acquired input data consisting of a time series of 2D images at each z position along the heart volume, to produce a time sequence of 3D volumes of the beating heart. The study includes a novel robust validation technique, which quantitatively evaluates the accuracy of the gating technique, in addition to visual evaluations by 2D multiplanar reformatting (MPR) and 3D volume rendering. The retrospective gating and validation is demonstrated on a stage 14 embryonic quail heart data set. Using the validation scheme, it is shown that the gating is accurate within a standard deviation of 4.7 ms, which is an order of magnitude shorter than the time interval during which systolic contraction (approximately 50 ms) occurs in the developing embryo. This gating method has allowed, for the first time, clear visualization of systolic dynamics of the looping embryonic heart in 3D.

Semiautomatic segmentation and quantification of calcified plaques in intracoronary optical coherence tomography images

Coronary calcified plaque (CP) is both an important marker of atherosclerosis and major determinant of the success of coronary stenting. Intracoronary optical coherence tomography (OCT) with high spatial resolution can provide detailed volumetric characterization of CP. We present a semiautomatic method for segmentation and quantification of CP in OCT images. Following segmentation of the lumen, guide wire, and arterial wall, the CP was localized by edge detection and traced using a combined intensity and gradient-based level-set model. From the segmentation regions, quantification of the depth, area, angle fill fraction, and thickness of the CP was demonstrated. Validation by comparing the automatic results to expert manual segmentation of 106 in vivo images from eight patients showed an accuracy of 78±9%. For a variety of CP measurements, the bias was insignificant (except for depth measurement) and the agreement was adequate when the CP has a clear outer border and no guide-wire overlap. These results suggest that the proposed method can be used for automated CP analysis in OCT, thereby facilitating our understanding of coronary artery calcification in the process of atherosclerosis and helping guide complex interventional strategies in coronary arteries with superficial calcification.

3D Cryo-Imaging: A Very High-Resolution View of the Whole Mouse

We developed the Case Cryo‐imaging system that provides information rich, very high‐resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section‐and‐image block‐face imaging technology. The system consists of a mouse‐sized, motorized cryo‐microtome with special features for imaging, a modified, brightfield/fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 μm over the block face of a whole mouse sectioned at 40 μm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo‐imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo‐imaging, we could obtain 3D vasculature down to 10 μm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field‐of‐view, depth of field, contrast, and resolution, the Case Cryo‐imaging system fills the gap between whole animal in vivo imaging and histology. histology. Anat Rec, 292:342–351, 2009.

Denoising and 4D visualization of OCT images

We are using Optical Coherence Tomography (OCT) to image structure and function of the developing embryonic heart in avian models. Fast OCT imaging produces very large 3D (2D + time) and 4D (3D volumes + time) data sets, which greatly challenge ones ability to visualize results. Noise in OCT images poses additional challenges. We created an algorithm with a quick, data set specific optimization for reduction of both shot and speckle noise and applied it to 3D visualization and image segmentation in OCT. When compared to baseline algorithms (median, Wiener, orthogonal wavelet, basic non-orthogonal wavelet), a panel of experts judged the new algorithm to give much improved volume renderings concerning both noise and 3D visualization. Specifically, the algorithm provided a better visualization of the myocardial and endocardial surfaces, and the interaction of the embryonic heart tube with surrounding tissue. Quantitative evaluation using an image quality figure of merit also indicated superiority of th new algorithm. Noise reduction aided semi-automatic 2D image segmentation, as quantitatively evaluated using a contour distance measure with respect to an expert segmented contour. In conclusion, the noise reduction algorithm should be quite useful for visualization and quantitative measurements (e.g., heart volume, stroke volume, contraction velocity, etc.) in OCT embryo images. With its semi-automatic, data set specific optimization, we believe that the algorithm can be applied to OCT images from other applications.

Measuring hemodynamics in the developing heart tube with four-dimensional gated Doppler optical coherence tomography

Hemodynamics is thought to play a major role in heart development, yet tools to quantitatively assess hemodynamics in the embryo are sorely lacking. The especially challenging analysis of hemodynamics in the early embryo requires new technology. Small changes in blood flow could indicate when anomalies are initiated even before structural changes can be detected. Furthermore, small changes in the early embryo that affect blood flow could lead to profound abnormalities at later stages. We present a demonstration of 4-D Doppler optical coherence tomography (OCT) imaging of structure and flow, and present several new hemodynamic measurements on embryonic avian hearts at early stages prior to the formation of the four chambers. Using 4-D data, pulsed Doppler measurements could accurately be attained in the inflow and outflow of the heart tube. Also, by employing an en-face slice from the 4-D Doppler image set, measurements of stroke volume and cardiac output are obtained without the need to determine absolute velocity. Finally, an image plane orthogonal to the blood flow is used to determine shear stress by calculating the velocity gradient normal to the endocardium. Hemodynamic measurements will be crucial to identifying genetic and environmental factors that lead to congenital heart defects.

Altered hypoxia-inducible factor-1 alpha expression levels correlate with coronary vessel anomalies.

The outflow tract myocardium and other regions corresponding to the location of the major coronary vessels of the developing chicken heart, display a high level of hypoxia as assessed by the hypoxia indicator EF5. The EF5‐positive tissues were also specifically positive for nuclear‐localized hypoxia inducible factor‐1 alpha (HIF‐1α), the oxygen‐sensitive component of the hypoxia inducible factor‐1 (HIF‐1) heterodimer. This led to our hypothesis that there is a “template” of hypoxic tissue that determines the stereotyped pattern of the major coronary vessels. In this study, we disturbed this template by altering ambient oxygen levels (hypoxia 15%; hyperoxia 75–40%) during the early phases of avian coronary vessel development, in order to alter tissue hypoxia, HIF‐1α protein expression, and its downstream target genes without high mortality. We also altered HIF‐1α gene expression in the embryonic outflow tract cardiomyocytes by injecting an adenovirus containing a constitutively active form of HIF‐1α (AdCA5). We assayed for coronary anomalies using anti‐alpha‐smooth muscle actin immunohistology. When incubated under abnormal oxygen levels or injected with a low titer of the AdCA5, coronary arteries displayed deviations from their normal proximal connections to the aorta. These deviations were similar to known clinical anomalies of coronary arteries. These findings indicated that developing coronary vessels may be subject to a level of regulation that is dependent on differential oxygen levels within cardiac tissues and subsequent HIF‐1 regulation of gene expression. Developmental Dynamics 238:2688–2700, 2009.

Automatic stent detection in intravascular OCT images using bagged decision trees

Intravascular optical coherence tomography (iOCT) is being used to assess viability of new coronary artery stent designs. We developed a highly automated method for detecting stent struts and measuring tissue coverage. We trained a bagged decision trees classifier to classify candidate struts using features extracted from the images. With 12 best features identified by forward selection, recall (precision) were 90%–94% (85%–90%). Including struts deemed insufficiently bright for manual analysis, precision improved to 94%. Strut detection statistics approached variability of manual analysis. Differences between manual and automatic area measurements were 0.12 ± 0.20 mm2 and 0.11 ± 0.20 mm2 for stent and tissue areas, respectively. With proposed algorithms, analyst time per stent should significantly reduce from the 6–16 hours now required.

Whole mouse cryo-imaging

The Case cryo-imaging system is a section and image system which allows one to acquire micron-scale, information rich, whole mouse color bright field and molecular fluorescence images of an entire mouse. Cryo-imaging is used in a variety of applications, including mouse and embryo anatomical phenotyping, drug delivery, imaging agents, metastastic cancer, stem cells, and very high resolution vascular imaging, among many. Cryo-imaging fills the gap between whole animal in vivo imaging and histology, allowing one to image a mouse along the continuum from the mouse -> organ -> tissue structure -> cell -> sub-cellular domains. In this overview, we describe the technology and a variety of exciting applications. Enhancements to the system now enable tiled acquisition of high resolution images to cover an entire mouse. High resolution fluorescence imaging, aided by a novel subtraction processing algorithm to remove sub-surface fluorescence, makes it possible to detect fluorescently-labeled single cells. Multi-modality experiments in Magnetic Resonance Imaging and Cryo-imaging of a whole mouse demonstrate superior resolution of cryo-images and efficiency of registration techniques. The 3D results demonstrate the novel true-color volume visualization tools we have developed and the inherent advantage of cryo-imaging in providing unlimited depth of field and spatial resolution. The recent results continue to demonstrate the value cryo-imaging provides in the field of small animal imaging research.