3D Volume Sets Research Articles

Application of transport-based metric for continuous interpolation between cryo-EM density maps.

Cryogenic electron microscopy (cryo-EM) has become widely used for the past few years in structural biology, to collect single images of macromolecules “frozen in time”. As this technique facilitates the identification of multiple conformational states adopted by the same molecule, a direct product of it is a set of 3D volumes, also called EM maps. To gain more insights on the possible mechanisms that govern transitions between different states, and hence the mode of action of a molecule, we recently introduced a bioinformatic tool that interpolates and generates morphing trajectories joining two given EM maps. This tool is based on recent advances made in optimal transport, that allow efficient evaluation of Wasserstein barycenters of 3D shapes. As the overall performance of the method depends on various key parameters, including the sensitivity of the regularization parameter, we performed various numerical experiments to demonstrate how MorphOT can be applied in different contexts and settings. Finally, we discuss current limitations and further potential connections between other optimal transport theories and the conformational heterogeneity problem inherent with cryo-EM data.

Estimation of dynamic time activity curves from dynamic cardiac SPECT imaging

Whole-heart coronary flow reserve (CFR) may be useful as an early predictor of cardiovascular disease or heart failure. Here we propose a simple method to extract the time-activity curve, an essential component needed for estimating the CFR, for a small number of compartments in the body, such as normal myocardium, blood pool, and ischemic myocardial regions, from SPECT data acquired with conventional cameras using slow rotation.We evaluated the method using a realistic simulation of 99mTc-teboroxime imaging. Uptake of 99mTc-teboroxime based on data from the literature were modeled. Data were simulated using the anatomically-realistic 3D NCAT phantom and an analytic projection code that realistically models attenuation, scatter, and the collimator-detector response. The proposed method was then applied to estimate time activity curves (TACs) for a set of 3D volumes of interest (VOIs) directly from the projections. We evaluated the accuracy and precision of estimated TACs and studied the effects of the presence of perfusion defects that were and were not modeled in the estimation procedure.The method produced good estimates of the myocardial and blood-pool TACS organ VOIs, with average weighted absolute biases of less than 5% for the myocardium and 10% for the blood pool when the true organ boundaries were known and the activity distributions in the organs were uniform. In the presence of unknown perfusion defects, the myocardial TAC was still estimated well (average weighted absolute bias <10%) when the total reduction in myocardial uptake (product of defect extent and severity) was ≤5%. This indicates that the method was robust to modest model mismatch such as the presence of moderate perfusion defects and uptake nonuniformities. With larger defects where the defect VOI was included in the estimation procedure, the estimated normal myocardial and defect TACs were accurate (average weighted absolute bias ≈5% for a defect with 25% extent and 100% severity).

Intensive training program for ultrasound diagnosis of adnexal masses: protocol and preliminary results

To assess the feasibility of a specific training program for ultrasound diagnosis of adnexal masses. A 2-month intensive training program was developed. The program protocol consisted of a 1-day intensive theoretical course focused on clinical and sonographic issues related to adnexal masses and ovarian cancer, followed by a 4-week real-time ultrasound training program in a tertiary center (25-30 adnexal masses evaluated per month) and a final 4-week period for offline assessment of three-dimensional (3D) volumes from adnexal masses. In this final period, each trainee evaluated five sets of 100 3D volumes. 3D volumes contained gray-scale and power Doppler information, and the trainee was provided with clinical data for each case (patient age, menopausal status and reported symptoms). 3D volumes were obtained from surgically removed masses that had undergone histological diagnosis or from masses that had been followed up until resolution. After assessment of each set, the trainee's diagnostic performance was calculated (sensitivity and specificity) and each incorrectly classified mass was evaluated with the trainer. The objective was to achieve a sensitivity of > 95% and a specificity of > 90%. Learning curve cumulative summation (LC-CUSUM) graphs were plotted to assess the learning curve for the trainees. One trainer and two trainees with little experience in gynecological ultrasound (one gynecologist and one radiologist) participated in this study. LC-CUSUM graphs showed that competence was achieved after 170 or 185 examinations. The objectives for diagnostic performance were achieved after assessment of the second set of 3D volumes (200 cases) for each trainee. The proposed training program appears to be feasible. High diagnostic performance can be achieved after analysis of 200 cases and maintained thereafter.

Optimizing tool selection

Selecting optimal cutting tools that can answer to the performance criteria of manufacturing economics (quality, productivity, cost, etc) is an important step in planning the manufacture of components. Achieving this, however, is difficult because of the many constraints involved in the tool selection process. This paper describes a method for determining a theoretical optimal combination of cutting tools given a set of 3D volumes or 2D profiles. Optimal tools are selected by considering residual material that is inaccessible to oversized cutters and the relative clearance rates of cutters that can access these regions of the selected machining features. The current implementation described does not give exact results because several machining parameters have been ignored during the selection process, such as tool path length, plunge rates, etc. However, the experimental studies carried out to verify the theoretical results suggest that while these factors may influence the absolute values calculated, in general, their influence on the relative ranking of the tools is insignificant. The results presented here suggest that the 'correct' combination of tools could significantly reduce machining times. Consequently, the paper concludes with a discussion of how modifications to typical tool path generation routines in commercial CAM systems could improve productivity.