Developing both graphical and command-line user interfaces for neuroimaging algorithms requires considerable effort. Neuroimaging algorithms can meet their potential only if they can be easily and frequently used by their intended users. Deployment of a large suite of such algorithms on multiple platforms requires consistency of user interface controls, consistent results across various platforms and thorough testing. We present the design and implementation of a novel object-oriented framework that allows for rapid development of complex image analysis algorithms with many reusable components and the ability to easily add graphical user interface controls. Our framework also allows for simplified yet robust nightly testing of the algorithms to ensure stability and cross platform interoperability. All of the functionality is encapsulated into a software object requiring no separate source code for user interfaces, testing or deployment. This formulation makes our framework ideal for developing novel, stable and easy-to-use algorithms for medical image analysis and computer assisted interventions. The framework has been both deployed at Yale and released for public use in the open source multi-platform image analysis software-BioImage Suite (bioimagesuite.org).
Collagen XI alpha 1 (Col11a1) is an extracellular matrix molecule required for embryonic development with a role in both nucleating the formation of fibrils and regulating the diameter of heterotypic fibrils during collagen fibrillar assembly. Although found in many different tissues throughout the vertebrate body, Col11a1 plays an essential role in endochondral ossification. To further understand the function of Col11a1 in the process of bone formation, we compared skeletal mineralization in wild-type (WT) mice and Col11a1-deficient mice using X-ray microtomography (micro-CT) and histology. Changes in trabecular bone microstructure were observed and are presented here. Additionally, changes to the periosteal bone collar of developing long bones were observed and resulted in an increase in thickness in the case of Col11a1-deficient mice compared to WT littermates. Vertebral bodies were incompletely formed in the absence of Col11a1. The data demonstrate that Col11a1 depletion results in alteration to newly-formed bone and is consistent with a role for Col11a1 in mineralization. These findings indicate that expression of Col11a1 in the growth plate and perichondrium is essential for trabecular bone and bone collar formation during endochondral ossification. The observed changes to mineralized tissues further define the function of Col11a1.
The effective visualization of vascular structures is critical for diagnosis, surgical planning as well as treatment evaluation. In recent work, we have developed an algorithm for vessel detection that examines the intensity profile around each voxel in an angiographic image and determines the likelihood that any given voxel belongs to a vessel; we term this the "vesselness coefficient" of the voxel. Our results show that our algorithm works particularly well for visualizing branch points in vessels. Compared to standard Hessian based techniques, which are fine-tuned to identify long cylindrical structures, our technique identifies branches and connections with other vessels.Using our computed vesselness coefficient, we explore a set of techniques for visualizing vasculature. Visualizing vessels is particularly challenging because not only is their position in space important for clinicians but it is also important to be able to resolve their spatial relationship. We applied visualization techniques that provide shape cues as well as depth cues to allow the viewer to differentiate between vessels that are closer from those that are farther. We use our computed vesselness coefficient to effectively visualize vasculature in both clinical neurovascular x-ray computed tomography based angiography images, as well as images from three different animal studies. We conducted a formal user evaluation of our visualization techniques with the help of radiologists, surgeons, and other expert users. Results indicate that experts preferred distance color blending and tone shading for conveying depth over standard visualization techniques.
Traditionally, time-varying data has been visualized using snapshots of the individual time steps or an animation of the snapshots shown in a sequential manner. For larger datasets with many timevarying features, animation can be limited in its use, as an observer can only track a limited number of features over the last few frames. Visually inspecting each snapshot is not practical either for a large number of time-steps.We propose new techniques inspired from the illustration literature to convey change over time more effectively in a time-varying dataset. Speedlines are used extensively by cartoonists to convey motion, speed, or change over different panels. Flow ribbons are another technique used by cartoonists to depict motion in a single frame. Strobe silhouettes are used to depict previous positions of an object to convey the previous positions of the object to the user. These illustration-inspired techniques can be used in conjunction with animation to convey change over time.
Traditionally, time-varying data has been visualized using snapshots of the individual time steps or an animation of the snapshots shown in a sequential manner. For larger datasets with many timevarying features, animation can be limited in its use, as an observer can only track a limited number of features over the last few frames. Visually inspecting each snapshot is not practical either for a large number of time-steps.We propose new techniques inspired from the illustration literature to convey change over time more effectively in a time-varying dataset. Speedlines are used extensively by cartoonists to convey motion, speed, or change over different panels. Flow ribbons are another technique used by cartoonists to depict motion in a single frame. Strobe silhouettes are used to depict previous positions of an object to convey the previous positions of the object to the user. These illustration-inspired techniques can be used in conjunction with animation to convey change over time.
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