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

FReLU: Flexible Rectified Linear Units for Improving Convolutional Neural Networks

Rectified linear unit (ReLU) is a widely used activation function for deep convolutional neural networks. However, because of the zero-hard rectification, ReLU networks miss the benefits from negative values. In this paper, we propose a novel activation function called \emph{flexible rectified linear unit (FReLU)} to further explore the effects of negative values. By redesigning the rectified point of ReLU as a learnable parameter, FReLU expands the states of the activation output. When the network is successfully trained, FReLU tends to converge to a negative value, which improves the expressiveness and thus the performance. Furthermore, FReLU is designed to be simple and effective without exponential functions to maintain low cost computation. For being able to easily used in various network architectures, FReLU does not rely on strict assumptions by self-adaption. We evaluate FReLU on three standard image classification datasets, including CIFAR-10, CIFAR-100, and ImageNet. Experimental results show that the proposed method achieves fast convergence and higher performances on both plain and residual networks

Robust Depth Linear Error Decomposition with Double Total Variation and Nuclear Norm for Dynamic MRI Reconstruction

Compressed Sensing (CS) significantly speeds up Magnetic Resonance Image (MRI) processing and achieves accurate MRI reconstruction from under-sampled k-space data. According to the current research, there are still several problems with dynamic MRI k-space reconstruction based on CS. 1) There are differences between the Fourier domain and the Image domain, and the differences between MRI processing of different domains need to be considered. 2) As three-dimensional data, dynamic MRI has its spatial-temporal characteristics, which need to calculate the difference and consistency of surface textures while preserving structural integrity and uniqueness. 3) Dynamic MRI reconstruction is time-consuming and computationally resource-dependent. In this paper, we propose a novel robust low-rank dynamic MRI reconstruction optimization model via highly under-sampled and Discrete Fourier Transform (DFT) called the Robust Depth Linear Error Decomposition Model (RDLEDM). Our method mainly includes linear decomposition, double Total Variation (TV), and double Nuclear Norm (NN) regularizations. By adding linear image domain error analysis, the noise is reduced after under-sampled and DFT processing, and the anti-interference ability of the algorithm is enhanced. Double TV and NN regularizations can utilize both spatial-temporal characteristics and explore the complementary relationship between different dimensions in dynamic MRI sequences. In addition, Due to the non-smoothness and non-convexity of TV and NN terms, it is difficult to optimize the unified objective model. To address this issue, we utilize a fast algorithm by solving a primal-dual form of the original problem. Compared with five state-of-the-art methods, extensive experiments on dynamic MRI data demonstrate the superior performance of the proposed method in terms of both reconstruction accuracy and time complexity

Spatial residual blocks combined parallel network for hyperspectral image classification.

In hyperspectral image (HSI) classification, there are challenges of the spatial variation in spectral features and the lack of labeled samples. In this paper, a novel spatial residual blocks combined parallel network (SRPNet) is proposed for HSI classification. Firstly, the spatial residual blocks extract spatial features from rich spatial contexts information, which can be used to deal with the spatial variation of spectral signatures. Especially, the skip connection in spatial residual blocks is conducive to the backpropagation of gradients and mitigates the declining-accuracy phenomenon in the deep network. Secondly, the parallel structure is employed to extract spectral features. Spectral feature learning on parallel branches contains fewer independent connection weighs through parameter sharing. Thus, fewer parameters of the network require a lesser number of training samples. Furthermore, the feature fusion is conducted on the multi-scale features from different layers in the spectral feature learning part. Extensive experiments of three representative HSI data sets illustrate the effectiveness of the proposed network

To Deconvolve, or Not to Deconvolve: Inferences of Neuronal Activities using Calcium Imaging Data

With the increasing popularity of calcium imaging data in neuroscience research, methods for analyzing calcium trace data are critical to address various questions. The observed calcium traces are either analyzed directly or deconvolved to spike trains to infer neuronal activities. When both approaches are applicable, it is unclear whether deconvolving calcium traces is a necessary step. In this article, we compare the performance of using calcium traces or their deconvolved spike trains for three common analyses: clustering, principal component analysis (PCA), and population decoding. Our simulations and applications to real data suggest that the estimated spike data outperform calcium trace data for both clustering and PCA. Although calcium trace data show higher predictability than spike data at each time point, spike history or cumulative spike counts is comparable to or better than calcium traces in population decoding

Interpretable emotion recognition using EEG signals

Electroencephalogram (EEG) signal-based emotion recognition has attracted wide interests in recent years and has been broadly adopted in medical, affective computing, and other relevant fields. However, the majority of the research reported in this field tends to focus on the accuracy of classification whilst neglecting the interpretability of emotion progression. In this paper, we propose a new interpretable emotion recognition approach with the activation mechanism by using machine learning and EEG signals. This paper innovatively proposes the emotional activation curve to demonstrate the activation process of emotions. The algorithm first extracts features from EEG signals and classifies emotions using machine learning techniques, in which different parts of a trial are used to train the proposed model and assess its impact on emotion recognition results. Second, novel activation curves of emotions are constructed based on the classification results, and two emotion coefficients, i.e., the correlation coefficients and entropy coefficients. The activation curve can not only classify emotions but also reveals to a certain extent the emotional activation mechanism. Finally, a weight coefficient is obtained from the two coefficients to improve the accuracy of emotion recognition. To validate the proposed method, experiments have been carried out on the DEAP and SEED dataset. The results support the point that emotions are progressively activated throughout the experiment, and the weighting coefficients based on the correlation coefficient and the entropy coefficient can effectively improve the EEG-based emotion recognition accuracy