Semiautomated Skeletonization of the Pulmonary Arterial Tree in Micro-CT Images

We present a simple and robust approach that utilizes planar images at different angular rotations combined with unfiltered back-projection to locate the central axes of the pulmonary arterial tree. Three-dimensional points are selected interactively by the user. The computer calculates a sub- volume unfiltered back-projection orthogonal to the vector connecting the two points and centered on the first point. Because more x-rays are absorbed at the thickest portion of the vessel, in the unfiltered back-projection, the darkest pixel is assumed to be the center of the vessel. The computer replaces this point with the newly computer-calculated point. A second back-projection is calculated around the original point orthogonal to a vector connecting the newly-calculated first point and user-determined second point. The darkest pixel within the reconstruction is determined. The computer then replaces the second point with the XYZ coordinates of the darkest pixel within this second reconstruction. Following a vector based on a moving average of previously determined 3- dimensional points along the vessel\u27s axis, the computer continues this skeletonization process until stopped by the user. The computer estimates the vessel diameter along the set of previously determined points using a method similar to the full width-half max algorithm. On all subsequent vessels, the process works the same way except that at each point, distances between the current point and all previously determined points along different vessels are determined. If the difference is less than the previously estimated diameter, the vessels are assumed to branch. This user/computer interaction continues until the vascular tree has been skeletonized

High-throughput hyperdimensional vertebrate phenotyping

Most gene mutations and biologically active molecules cause complex responses in animals that cannot be predicted by cell culture models. Yet animal studies remain too slow and their analyses are often limited to only a few readouts. Here we demonstrate high-throughput optical projection tomography with micrometre resolution and hyperdimensional screening of entire vertebrates in tens of seconds using a simple fluidic system. Hundreds of independent morphological features and complex phenotypes are automatically captured in three dimensions with unprecedented speed and detail in semitransparent zebrafish larvae. By clustering quantitative phenotypic signatures, we can detect and classify even subtle alterations in many biological processes simultaneously. We term our approach hyperdimensional in vivo phenotyping. To illustrate the power of hyperdimensional in vivo phenotyping, we have analysed the effects of several classes of teratogens on cartilage formation using 200 independent morphological measurements, and identified similarities and differences that correlate well with their known mechanisms of actions in mammals.National Institutes of Health (U.S.) (NIH Transformative Research Award (R01 NS073127))National Institutes of Health (U.S.) (NIH (R01 GM095672)National Institutes of Health (U.S.) (NIH Director’s New Innovator award (1-DP2-OD002989))Howard Hughes Medical Institute (International Student Fellowship)Broad Institute of MIT and Harvard (SPARC grant)David & Lucile Packard Foundation (Award in Science and Engineering

Toolbox for in vivo imaging of host-parasite interactions at multiple scales

Animal models have for long been pivotal for parasitology research. Over the last few years, techniques such as intravital, optoacoustic and magnetic resonance imaging, optical projection tomography, and selective plane illumination microscopy developed promising potential for gaining insights into host-pathogen interactions by allowing different visualization forms in vivo and ex vivo. Advances including increased resolution, penetration depth, and acquisition speed, together with more complex image analysis methods, facilitate tackling biological problems previously impossible to study and/or quantify. Here we discuss advances and challenges in the in vivo imaging toolbox, which hold promising potential for the field of parasitology

Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions

Fusion of 3D QCA and IVUS/OCT

The combination/fusion of quantitative coronary angiography (QCA) and intravascular ultrasound (IVUS)/optical coherence tomography (OCT) depends to a great extend on the co-registration of X-ray angiography (XA) and IVUS/OCT. In this work a new and robust three-dimensional (3D) segmentation and registration approach is presented and validated. The approach starts with standard QCA of the vessel of interest in the two angiographic views (either biplane or two monoplane views). Next, the vessel of interest is reconstructed in 3D and registered with the corresponding IVUS/OCT pullback series by a distance mapping algorithm. The accuracy of the registration was retrospectively evaluated on 12 silicone phantoms with coronary stents implanted, and on 24 patients who underwent both coronary angiography and IVUS examinations of the left anterior descending artery. Stent borders or sidebranches were used as markers for the validation. While the most proximal marker was set as the baseline position for the distance mapping algorithm, the subsequent markers were used to evaluate the registration error. The correlation between the registration error and the distance from the evaluated marker to the baseline position was analyzed. The XA-IVUS registration error for the 12 phantoms was 0.03 ± 0.32 mm (P = 0.75). One OCT pullback series was excluded from the phantom study, since it did not cover the distal stent border. The XA-OCT registration error for the remaining 11 phantoms was 0.05 ± 0.25 mm (P = 0.49). For the in vivo validation, two patients were excluded due to insufficient image quality for the analysis. In total 78 sidebranches were identified from the remaining 22 patients and the registration error was evaluated on 56 markers. The registration error was 0.03 ± 0.45 mm (P = 0.67). The error was not correlated to the distance between the evaluated marker and the baseline position (P = 0.73). In conclusion, the new XA-IVUS/OCT co-registration approach is a straightforward and reliable solution to combine X-ray angiography and IVUS/OCT imaging for the assessment of the extent of coronary artery disease. It provides the interventional cardiologist with detailed information about vessel size and plaque size at every position along the vessel of interest, making this a suitable tool during the actual intervention

High-throughput hyperdimensional vertebrate phenotyping

Most gene mutations and biologically active molecules cause complex responses in animals that cannot be predicted by cell culture models. Yet animal studies remain too slow and their analyses are often limited to only a few readouts. Here we demonstrate high-throughput optical projection tomography with micrometer resolution and hyperdimensional screening of entire vertebrates in tens of seconds using a simple fluidic system. Hundreds of independent morphological features and complex phenotypes are automatically captured in three dimensions with unprecedented speed and detail in semi-transparent zebrafish larvae. By clustering quantitative phenotypic signatures, we can detect and classify even subtle alterations in many biological processes simultaneously. We term our approach hyperdimensional in vivo phenotyping (HIP). To illustrate the power of HIP, we have analyzed the effects of several classes of teratogens on cartilage formation using 200 independent morphological measurements and identified similarities and differences that correlate well with their known mechanisms of actions in mammals