M. Gopi

Nitin Agarwal, M Gopi

We present a new meshing algorithm called guided and augmented meshing, GAMesh, which uses a mesh prior to generate a surface for the output points of a point network. By projecting the output points onto this prior and simplifying the resulting mesh, GAMesh ensures a surface with the same topology as the mesh prior but whose geometric fidelity is controlled by the point network. This makes GAMesh independent of both the density and distribution of the output points, a common artifact in traditional surface reconstruction algorithms. We show that such a separation of geometry from topology can have several advantages especially in single-view shape prediction, fair evaluation of point networks and reconstructing surfaces for networks which output sparse point clouds. We further show that by training point networks with GAMesh, we can directly optimize the vertex positions to generate adaptive meshes with arbitrary topologies.

Nitin Agarwal, Sung-eui Yoon, M Gopi

Sharp features such as edges and corners play an important role in the perception of 3D models. In order to capture them better, we propose quadric loss, a point-surface loss function, which minimizes the quadric error between the reconstructed points and the input surface. Computation of Quadric loss is easy, efficient since the quadric matrices can be computed apriori, and is fully differentiable, making quadric loss suitable for training point and mesh based architectures. Through extensive experiments we show the merits and demerits of quadric loss. When combined with Chamfer loss, quadric loss achieves better reconstruction results as compared to any one of them or other point-surface loss functions.

Zahra Montazeri, Gopi M

Manual preparation of tissue slices for microscopy imaging can introduce tissue tears and overlaps. Typically, further digital processing algorithms such as registration and 3D reconstruction from tissue image stacks cannot handle images with tissue tear/overlap artifacts, and so such images are usually discarded. In this paper, we propose an imaging model and an algorithm to digitally separate overlapping tissue data of mouse brain images into two layers. We show the correctness of our model and the algorithm by comparing our results with the ground truth.

Nitin Agarwal, Xiangmin Xu, Gopi Meenakshisundaram

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.