Improved Orientation Sampling for Indexing Diffraction Patterns of Polycrystalline Materials

Orientation mapping is a widely used technique for revealing the microstructure of a polycrystalline sample. The crystalline orientation at each point in the sample is determined by analysis of the diffraction pattern, a process known as pattern indexing. A recent development in pattern indexing is the use of a brute-force approach, whereby diffraction patterns are simulated for a large number of crystalline orientations, and compared against the experimentally observed diffraction pattern in order to determine the most likely orientation. Whilst this method can robust identify orientations in the presence of noise, it has very high computational requirements. In this article, the computational burden is reduced by developing a method for nearly-optimal sampling of orientations. By using the quaternion representation of orientations, it is shown that the optimal sampling problem is equivalent to that of optimally distributing points on a four-dimensional sphere. In doing so, the number of orientation samples needed to achieve a indexing desired accuracy is significantly reduced. Orientation sets at a range of sizes are generated in this way for all Laue groups, and are made available online for easy use.Comment: 11 pages, 7 figure

Development of airborne hemispheric spectrometer

A new concept of hyperspectral instrument is presented. Novel design of hyperspectral skydome allows retrieval of atmospheric constituents and properties from a snapshot of spectral solar radiation over entire sky, regardless of platform motion either on ground or aircraft. Design and description of subsystems of the instrument are given followed by preliminary tolerance analysis, whose results are to be added in the retrieval algorithm along with hardware specifications. Extended application of the hyperspectral skydome is being carried out filling in the gap in the imaging spectrometry

Implicit-PDF: Non-Parametric Representation of Probability Distributions on the Rotation Manifold

Single image pose estimation is a fundamental problem in many vision and robotics tasks, and existing deep learning approaches suffer by not completely modeling and handling: i) uncertainty about the predictions, and ii) symmetric objects with multiple (sometimes infinite) correct poses. To this end, we introduce a method to estimate arbitrary, non-parametric distributions on SO(3). Our key idea is to represent the distributions implicitly, with a neural network that estimates the probability given the input image and a candidate pose. Grid sampling or gradient ascent can be used to find the most likely pose, but it is also possible to evaluate the probability at any pose, enabling reasoning about symmetries and uncertainty. This is the most general way of representing distributions on manifolds, and to showcase the rich expressive power, we introduce a dataset of challenging symmetric and nearly-symmetric objects. We require no supervision on pose uncertainty -- the model trains only with a single pose per example. Nonetheless, our implicit model is highly expressive to handle complex distributions over 3D poses, while still obtaining accurate pose estimation on standard non-ambiguous environments, achieving state-of-the-art performance on Pascal3D+ and ModelNet10-SO(3) benchmarks

Reconstructing continuous distributions of 3D protein structure from cryo-EM images

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and randomly oriented two-dimensional projections. However, the imaged protein complexes may exhibit structural variability, which complicates reconstruction and is typically addressed using discrete clustering approaches that fail to capture the full range of protein dynamics. Here, we introduce a novel method for cryo-EM reconstruction that extends naturally to modeling continuous generative factors of structural heterogeneity. This method encodes structures in Fourier space using coordinate-based deep neural networks, and trains these networks from unlabeled 2D cryo-EM images by combining exact inference over image orientation with variational inference for structural heterogeneity. We demonstrate that the proposed method, termed cryoDRGN, can perform ab initio reconstruction of 3D protein complexes from simulated and real 2D cryo-EM image data. To our knowledge, cryoDRGN is the first neural network-based approach for cryo-EM reconstruction and the first end-to-end method for directly reconstructing continuous ensembles of protein structures from cryo-EM images

A novel sampling theorem on the rotation group

We develop a novel sampling theorem for functions defined on the three-dimensional rotation group SO(3) by connecting the rotation group to the three-torus through a periodic extension. Our sampling theorem requires $4L^3$ samples to capture all of the information content of a signal band-limited at $L$, reducing the number of required samples by a factor of two compared to other equiangular sampling theorems. We present fast algorithms to compute the associated Fourier transform on the rotation group, the so-called Wigner transform, which scale as $O(L^4)$, compared to the naive scaling of $O(L^6)$. For the common case of a low directional band-limit $N$, complexity is reduced to $O(N L^3)$. Our fast algorithms will be of direct use in speeding up the computation of directional wavelet transforms on the sphere. We make our SO3 code implementing these algorithms publicly available.Comment: 5 pages, 2 figures, minor changes to match version accepted for publication. Code available at http://www.sothree.or