Neural Information Processing Systems http://nips.cc/

DSC-MRI perfusion is a medical imaging technique for diagnosing and prognosing brain tumors and strokes. Its analysis relies on mathematical deconvolution, but noise or motion artifacts in a clinical environment can disrupt this process, leading to incorrect estimate of perfusion parameters. Although deep learning approaches have shown promising results, their calibration typically rely on third-party deconvolution algorithms to generate reference outputs and are bound to reproduce their limitations. To adress this problem, we propose a physics-informed autoencoder that leverages an analytical model to decode the perfusion parameters and guide the learning of the encoding network. This autoencoder is trained in a self-supervised fashion without any third-party software and its performance is evaluated on a database with glioma patients. Our method shows reliable results for glioma grading in accordance with other well-known deconvolution algorithms despite a lower computation time. It also achieved competitive performance even in the presence of high noise which is critical in a medical environment.

A recent study published in Nature Communications comprehensively evaluated computational methods used for spatial transcriptomics data analysis. The scientists investigated how well various advanced computer methods performed on real and simulated datasets and recommended which method to use depending on the type of analysis required. The guidelines may be helpful to researchers who want to improve the accuracy of their cellular analysis and understand complex tissue structures. The study has the potential to significantly transform how researchers approach spatial transcriptomics, ultimately advancing the understanding of how cells function in different tissues. Traditionally, gene expression is measured in bulk tissues providing an average mRNA expression level of mRNAs across all cells and all cell types in the tissue.

Calcium imaging is a critical tool for measuring the activity of large neural populations. Much effort has been devoted to developing "pre-processing" tools for calcium video data, addressing the important issues of e.g., motion correction, denoising, compression, demixing, and deconvolution. However, statistical modeling of deconvolved calcium signals (i.e., the estimated activity extracted by a pre-processing pipeline) is just as critical for interpreting calcium measurements, and for incorporating these observations into downstream probabilistic encoding and decoding models. Surprisingly, these issues have to date received significantly less attention. In this work we examine the statistical properties of the deconvolved activity estimates, and compare probabilistic models for these random signals. In particular, we propose a zero-inflated gamma (ZIG) model, which characterizes the calcium responses as a mixture of a gamma distribution and a point mass that serves to model zero responses. We apply the resulting models to neural encoding and decoding problems. We find that the ZIG model outperforms simpler models (e.g., Poisson or Bernoulli models) in the context of both simulated and real neural data, and can therefore play a useful role in bridging calcium imaging analysis methods with tools for analyzing activity in large neural populations.

In this paper, we present a deep convolutional neural network to capture the inherent properties of image degradation, which can handle different kernels and saturated pixels in a unified framework. The proposed neural network is motivated by the low-rank property of pseudo-inverse kernels. We first compute a generalized low-rank approximation for a large number of blur kernels, and then use separable filters to initialize the convolutional parameters in the network. Our analysis shows that the estimated decomposed matrices contain the most essential information of the input kernel, which ensures the proposed network to handle various blurs in a unified framework and generate high-quality deblurring results. Experimental results on benchmark datasets with noise and saturated pixels demonstrate that the proposed algorithm performs favorably against state-of-the-art methods.

In this paper, we present a deep convolutional neural network to capture the inherent properties of image degradation, which can handle different kernels and saturated pixels in a unified framework. The proposed neural network is motivated by the low-rank property of pseudo-inverse kernels. We first compute a generalized low-rank approximation for a large number of blur kernels, and then use separable filters to initialize the convolutional parameters in the network. Our analysis shows that the estimated decomposed matrices contain the most essential information of the input kernel, which ensures the proposed network to handle various blurs in a unified framework and generate high-quality deblurring results. Experimental results on benchmark datasets with noise and saturated pixels demonstrate that the proposed algorithm performs favorably against state-of-the-art methods.

In image deconvolution problems, the diagonalization of the underlying operators by means of the FFT usually yields very large speedups. When there are incomplete observations (e.g., in the case of unknown boundaries), standard deconvolution techniques normally involve non-diagonalizable operators, resulting in rather slow methods, or, otherwise, use inexact convolution models, resulting in the occurrence of artifacts in the enhanced images. In this paper, we propose a new deconvolution framework for images with incomplete observations that allows us to work with diagonalized convolution operators, and therefore is very fast. We iteratively alternate the estimation of the unknown pixels and of the deconvolved image, using, e.g., an FFT-based deconvolution method. This framework is an efficient, high-quality alternative to existing methods of dealing with the image boundaries, such as edge tapering. It can be used with any fast deconvolution method. We give an example in which a state-of-the-art method that assumes periodic boundary conditions is extended, through the use of this framework, to unknown boundary conditions. Furthermore, we propose a specific implementation of this framework, based on the alternating direction method of multipliers (ADMM). We provide a proof of convergence for the resulting algorithm, which can be seen as a "partial" ADMM, in which not all variables are dualized. We report experimental comparisons with other primal-dual methods, where the proposed one performed at the level of the state of the art. Four different kinds of applications were tested in the experiments: deconvolution, deconvolution with inpainting, superresolution, and demosaicing, all with unknown boundaries.

We consider the problem of estimating neural spikes from extracellular voltage recordings. Most current methods are based on clustering, which requires substantial human supervision and produces systematic errors by failing to properly handle temporally overlapping spikes. We formulate the problem as one of statistical inference, in which the recorded voltage is a noisy sum of the spike trains of each neuron convolved with its associated spike waveform. Joint maximum-a-posteriori (MAP) estimation of the waveforms and spikes is then a blind deconvolution problem in which the coefficients are sparse. We develop a block-coordinate descent method for approximating the MAP solution. We validate our method on data simulated according to the generative model, as well as on real data for which ground truth is available via simultaneous intracellular recordings. In both cases, our method substantially reduces the number of missed spikes and false positives when compared to a standard clustering algorithm, primarily by recovering temporally overlapping spikes. The method offers a fully automated alternative to clustering methods that is less susceptible to systematic errors.