Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

/pdf/features-and-development-of-coot-5al5bhwkg1.pdf

Features and development of Coot.

We present a new algorithm, called marching cubes, that creates triangle models of constant density surfaces from 3D medical data. Using a divide-and-conquer approach to generate inter-slice connectivity, we create a case table that defines triangle topology. The algorithm processes the 3D medical data in scan-line order and calculates triangle vertices using linear interpolation. We find the gradient of the original data, normalize it, and use it as a basis for shading the models. The detail in images produced from the generated surface models is the result of maintaining the inter-slice connectivity, surface data, and gradient information present in the original 3D data. Results from computed tomography (CT), magnetic resonance (MR), and single-photon emission computed tomography (SPECT) illustrate the quality and functionality of marching cubes. We also discuss improvements that decrease processing time and add solid modeling capabilities.

/pdf/marching-cubes-a-high-resolution-3d-surface-construction-3ealswkmtb.pdf

Marching cubes: A high resolution 3D surface construction algorithm

This paper surveys the field of augmented reality AR, in which 3D virtual objects are integrated into a 3D real environment in real time. It describes the medical, manufacturing, visualization, path planning, entertainment, and military applications that have been explored. This paper describes the characteristics of augmented reality systems, including a detailed discussion of the tradeoffs between optical and video blending approaches. Registration and sensing errors are two of the biggest problems in building effective augmented reality systems, so this paper summarizes current efforts to overcome these problems. Future directions and areas requiring further research are discussed. This survey provides a starting point for anyone interested in researching or using augmented reality.

/pdf/a-survey-of-augmented-reality-17irtaxt7z.pdf

A survey of augmented reality

MOLMOL: a program for display and analysis of macromolecular structures.

http://midag.cs.unc.edu/pubs/papers/Neuroimage06_Yushkevich.pdf

User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability

We describe a three-dimensional (3D) segmentation method that comprises (a) user interactive identification of tissue classes; (b) calculation of a probability distribution for each tissue; (c) creation of a feature map of the most probable tissues; (d) 3D segmentation of the magnetic resonance (MR) data; (e) smoothing of the segmented data; (f) extraction of surfaces of interest with connectivity; (g) generation of surfaces; and (h) rendering of multiple surfaces to plan surgery. Patients with normal head anatomy and with abnormalities such as multiple sclerosis lesions and brain tumors were scanned with a 1.5 T MR system using a two echo contiguous (interleaved), multislice pulse sequence that provides both proton density and T2-weighted contrast. After the user identified the tissues, the 3D data were automatically segmented into background, facial tissue, brain matter, CSF, and lesions. Surfaces of the face, brain, lateral ventricles, tumors, and multiple sclerosis lesions are displayed using color coding and gradient shading. Color improves the visualization of segmented tissues, while gradient shading enhances the perception of depth. Manipulation of the 3D model on a workstation aids surgical planning. Sulci and gyri stand out, thus aiding functional mapping of the brain surface.

Three-dimensional segmentation of MR images of the head using probability and connectivity.

PURPOSE: To develop a superconducting magnetic resonance (MR) imager that provides direct access to the patient and permits interactive MR-guided interventional procedures. MATERIALS AND METHODS: A 0.5-T superconducting magnet that allows a region of vertical access to the patient was designed and constructed. This magnet was integrated with newly designed shielded gradient coils, flexible surface coils, and nonmagnetic displays and with position-monitoring probes and device-tracking instrumentation. RESULTS: The magnet homogeneity was 12.3 ppm, and the gradient field was linear to within 1% over an imaging region 30 cm in diameter. The signal-to-noise ratio was 10% higher than in a comparable 0.5-T superconducting imager. Images were obtained in several anatomic regions with use of routine pulse sequences. Interactive image plane selection and near real-time imaging, with use of fast gradient-recalled echo sequences, were demonstrated at a rate of one image every 1.5 seconds. CONCLUSION: MR-guided interv...

Superconducting open-configuration MR imaging system for image-guided therapy.

Three‐dimensional (3‐D) surface reconstructions provide a method to view complex anatomy contained in a set of computed tomography(CT),magnetic resonance imaging(MRI), or single photon emission computed tomography tomograms. Existing methods of 3‐D display generate images based on the distance from an imaginary observation point to a patch on the surface and on the surface normal of the patch. We believe that the normalized gradient of the original values in the CT or MRI tomograms provides a better estimate for the surface normal and hence results in higher quality 3‐D images. Then two algorithms that generate 3‐D surface models are presented. The new methods use polygon and point primitives to interface with computer‐aided design equipment. Finally, several 3‐D images of both bony and soft tissue show the skull, spine, internal air cavities of the head and abdomen, and the abdominal aorta in detail.

Two algorithms for the three-dimensional reconstruction of tomograms.

A noninvasive method of tissue ablation that is guided and monitored with magnetic resonance (MR) imaging has been developed. The method uses sharply focused ultrasound transducers of different focal lengths to induce a localized temperature elevation during a short exposure (1-20 seconds). A hydraulic, computer-controlled positioning device moves the transducer in an MR imager. The positioner is built into a standard cradle in the imager. The system includes cavitation detection and power monitoring circuitry for patient safety. The target volume is outlined with cross-sectional MR images obtained immediately before sonication. By means of the software, the focus is moved to ablate the volume defined with the images. The temperature elevation during the exposure is monitored by means of the proton resonance frequency shift with fast gradient-echo sequences, and the necrosed volume is demonstrated with T2-weighted fast spin-echo images. This method has been extensively tested in in vivo animal experiments...

Harvey E. Cline

Papers

Marching cubes: A high resolution 3D surface construction algorithm

Three-dimensional segmentation of MR images of the head using probability and connectivity.

Superconducting open-configuration MR imaging system for image-guided therapy.

Two algorithms for the three-dimensional reconstruction of tomograms.

A clinical, noninvasive, MR imaging-monitored ultrasound surgery method.