Geometry Processing of Conventionally Produced Mouse Brain Slice Images

Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as an application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data.Comment: 14 pages, 11 figure

Real-time diffuse optical tomography using reduced-order light propagation models based on a priori anatomical and functional information

This paper proposes a new fast 3D image reconstruction algorithm for Diffuse Optical Tomography using reduced order polynomial mappings from the space of optical tissue parameters into the space of flux measurements at the detector locations. The polynomial mappings are constructed through an iterative estimation process involving structure detection, parameter estimation and cross-validation using data generated by simulating a diffusion approximation of the radiative transfer equation incorporating a priori anatomical and functional information provided by MR scans and prior psychological evidence. Numerical simulation studies demonstrate that reconstructed images are remarkably similar in quality as those obtained using the standard approach, but obtained at a fraction of the time

Atomic-scale grain boundary engineering to overcome hot-cracking in additively-manufactured superalloys

There are still debates regarding the mechanisms that lead to hot cracking in parts build by additive manufacturing (AM) of non-weldable Ni-based superalloys. This lack of in-depth understanding of the root causes of hot cracking is an impediment to designing engineering parts for safety-critical applications. Here, we deploy a near-atomic-scale approach to investigate the details of the compositional decoration of grain boundaries in the coarse-grained, columnar microstructure in parts built from a non-weldable Ni-based superalloy by selective electron-beam melting. The progressive enrichment in Cr, Mo and B at grain boundaries over the course of the AM-typical successive solidification and remelting events, accompanied by solid-state diffusion, causes grain boundary segregation induced liquation. This observation is consistent with thermodynamic calculations. We demonstrate that by adjusting build parameters to obtain a fine-grained equiaxed or a columnar microstructure with grain width smaller than 100 $\mu$m enables to avoid cracking, despite strong grain boundary segregation. We find that the spread of critical solutes to a higher total interfacial area, combined with lower thermal stresses, helps to suppress interfacial liquation.Comment: Accepted version at Acta Materiali

Fully automated segmentation and tracking of the intima media thickness in ultrasound video sequences of the common carotid artery

Abstract—The robust identification and measurement of the intima media thickness (IMT) has a high clinical relevance because it represents one of the most precise predictors used in the assessment of potential future cardiovascular events. To facilitate the analysis of arterial wall thickening in serial clinical investigations, in this paper we have developed a novel fully automatic algorithm for the segmentation, measurement, and tracking of the intima media complex (IMC) in B-mode ultrasound video sequences. The proposed algorithm entails a two-stage image analysis process that initially addresses the segmentation of the IMC in the first frame of the ultrasound video sequence using a model-based approach; in the second step, a novel customized tracking procedure is applied to robustly detect the IMC in the subsequent frames. For the video tracking procedure, we introduce a spatially coherent algorithm called adaptive normalized correlation that prevents the tracking process from converging to wrong arterial interfaces. This represents the main contribution of this paper and was developed to deal with inconsistencies in the appearance of the IMC over the cardiac cycle. The quantitative evaluation has been carried out on 40 ultrasound video sequences of the common carotid artery (CCA) by comparing the results returned by the developed algorithm with respect to ground truth data that has been manually annotated by clinical experts. The measured IMTmean ± standard deviation recorded by the proposed algorithm is 0.60 mm ± 0.10, with a mean coefficient of variation (CV) of 2.05%, whereas the corresponding result obtained for the manually annotated ground truth data is 0.60 mm ± 0.11 with a mean CV equal to 5.60%. The numerical results reported in this paper indicate that the proposed algorithm is able to correctly segment and track the IMC in ultrasound CCA video sequences, and we were encouraged by the stability of our technique when applied to data captured under different imaging conditions. Future clinical studies will focus on the evaluation of patients that are affected by advanced cardiovascular conditions such as focal thickening and arterial plaques