We consider the problem of high-dimensional light field reconstruction and develop a learning-based framework for spatial and angular super-resolution. Many current approaches either require disparity clues or restore the spatial and angular details separately. Such methods have difficulties with non-Lambertian surfaces or occlusions. In contrast, we formulate light field super-resolution (LFSR) as tensor restoration and develop a learning framework based on a two-stage restoration with 4-dimensional (4D) convolution. This allows our model to learn the features capturing the geometry information encoded in multiple adjacent views. Such geometric features vary near the occlusion regions and indicate the foreground object border. To train a feasible network, we propose a novel normalization operation based on a group of views in the feature maps, design a stage-wise loss function, and develop the multi-range training strategy to further improve the performance. Evaluations are conducted on a number of light field datasets including real-world scenes, synthetic data, and microscope light fields. The proposed method achieves superior performance and less execution time comparing with other state-of-the-art schemes.

New single-cell technologies continue to fuel the explosive growth in the scale of heterogeneous single-cell data. However, existing computational methods are inadequately scalable to large datasets and therefore cannot uncover the complex cellular heterogeneity. We introduce a highly scalable graph-based clustering algorithm PARC—Phenotyping by Accelerated Refined Community-partitioning—for large-scale, high-dimensional single-cell data (>1 million cells). Using large single-cell flow and mass cytometry, RNA-seq and imaging-based biophysical data, we demonstrate that PARC consistently outperforms state-of-the-art clustering algorithms without subsampling of cells, including Phenograph, FlowSOM and Flock, in terms of both speed and ability to robustly detect rare cell populations. For example, PARC can cluster a single-cell dataset of 1.1 million cells within 13 min, compared with >2 h for the next fastest graph-clustering algorithm. Our work presents a scalable algorithm to cope with increasingly large-scale single-cell analysis. https://github.com/ShobiStassen/PARC. Supplementary data are available at Bioinformatics online.

This article proposes an open-source hardware Posit Arithmetic Core Generator (PACoGen) for the recently developed universal number posit number system, along with a set of pipelined architectures. Posit number system composed of a run-time varying exponent component, which is defined by a composition of varying length “regime-bit„ and “exponent-bit„ (with a maximum size of ES bits, the exponent size). This in effect also makes the fraction part to vary at run-time in size and position. These run-time variations inherits an interesting hardware design challenge for posit arithmetic architectures. Posit number system, being at an infant stage of its development, possess very limited hardware solutions for its arithmetic architectures. In this view, this paper targets the algorithmic development and generic HDL generators (PACoGen) for basic posit arithmetic. The proposed open source PACoGen currently includes the adder/subtractor, multiplier and division arithmetic. PACoGen can provide the Verilog HDL code respective posit arithmetic for any given posit word-width (N) and exponent size (ES), as defined under the posit number system. Further, pipelined architectures of 32-bit posit with 6-bit exponent size are also proposed and discussed for addition/subtraction, multiplication and division arithmetic. The proposed posit arithmetic architectures are demonstrated on Virtex-7 (xc7vx330t-3ffg1157) FPGA device as well as Nangate 15nm ASIC platform. PACoGen would open a gateway for further posit arithmetic hardware exploration and evaluation.

Recent advances in ultra-high-throughput microscopy have enabled a new generation of cell classification methodologies using image-based cell phenotypes alone. In contrast to current single-cell analysis techniques that rely solely on slow and costly genetic/epigenetic analysis, these image-based analyses allow morphological profiling and screening of thousands or even millions of single cells at a fraction of the cost, and have been proven to demonstrate the statistical significance required for understanding the role of cell heterogeneity in diverse biological applications, ranging from cancer screening to drug candidate identification/validation processes. This paper examines the efficacies and opportunities presented by machine learning algorithms in processing large scale datasets with millions of label-free cell images. An automatic single-cell classification framework using convolutional neural network (CNN) has been developed. A comparative analysis of its efficiency in classifying large datasets against conventional k-nearest neighbors (kNN) and support vector machine (SVM) based methods are also presented. Experiments have shown that our proposed framework can efficiently identify multiple types cells with over 99% accuracy based on the phenotypic label-free bright-field images; and CNN-based models perform well and relatively stable against data volume compared with kNN and SVM.

This paper explores the design and implementation of BORPH, an operating system designed for FPGA-based reconfigurable computers. Hardware designs execute as normal UNIX processes under BORPH, having access to standard OS services, such as file system support. Hardware and software components of user designs may, therefore, run as communicating processes within BORPH's runtime environment. The familiar language independent UNIX kernel interface facilitates easy design reuse and rapid application development. To develop hardware designs, a Simulink-based design flow that integrates with BORPH is employed. Performances of BORPH on two on-chip systems implemented on a BEE2 platform are compared.