A spectral dissimilarity constrained nonnegative matrix factorization based cancer screening algorithm from hyperspectral fluorescence images

Bioluminescence from living body can help screen cancers without penetrating the inside of living body. Hyperspectral imaging technique is a novel way to obtain physical meaningful signatures, providing very fine spectral resolution, that can be very used in distinguishing different kinds of materials, and have been widely used in remote sensing field. Fluorescence imaging has proved effective in monitoring probable cancer cells. Recent work has made great progress on the hyperspectral fluorescence imaging techniques, which makes the elaborate spectral observation of cancer areas possible. So how to propose the proper hyperspectral image processing methods to handle the hyperspectral medical images is of practical importance. Cancer cells would be distinguishable with normal ones when the living body is injected with fluorescence, which helps organs inside the living body emit lights, and then the signals can be catched by the passive imaging sensor. Spectral unmixing technique in hyperspectral remote sensing has been introduced to detect the probable cancer areas. However, since the cancer areas are small and the normal areas and the cancer ares may not pure pixels so that the predefined endmembers would not available. In this case, the classic blind signals separation methods are applicable. Considering the spectral dissimilarity between cancer and normal cells, a novel spectral dissimilarity constrained based NMF method is proposed in this paper for cancer screening from fluorescence hyperspectral images. Experiments evaluate the performance of variable NMF based method and our proposed spectral dissimilarity based NMF methods: 1) The NMF methods do perform well in detect the cancer areas inside the living body; 2) The spectral dissimilarity constrained NMF present more accurate cancer areas; 3) The spectral dissimilarity constraint presents better performance in different SNR and different purities of the mixing endmembers. © 2012 IEEE

Nonlinear Hyperspectral Unmixing With Robust Nonnegative Matrix Factorization

International audienceWe introduce a robust mixing model to describe hyperspectral data resulting from the mixture of several pure spectral signatures. The new model extends the commonly used linear mixing model by introducing an additional term accounting for possible nonlinear effects, that are treated as sparsely distributed additive outliers.With the standard nonnegativity and sum-to-one constraints inherent to spectral unmixing, our model leads to a new form of robust nonnegative matrix factorization with a group-sparse outlier term. The factorization is posed as an optimization problem which is addressed with a block-coordinate descent algorithm involving majorization-minimization updates. Simulation results obtained on synthetic and real data show that the proposed strategy competes with state-of-the-art linear and nonlinear unmixing methods

Bayesian Nonparametric Unmixing of Hyperspectral Images

Hyperspectral imaging is an important tool in remote sensing, allowing for accurate analysis of vast areas. Due to a low spatial resolution, a pixel of a hyperspectral image rarely represents a single material, but rather a mixture of different spectra. HSU aims at estimating the pure spectra present in the scene of interest, referred to as endmembers, and their fractions in each pixel, referred to as abundances. Today, many HSU algorithms have been proposed, based either on a geometrical or statistical model. While most methods assume that the number of endmembers present in the scene is known, there is only little work about estimating this number from the observed data. In this work, we propose a Bayesian nonparametric framework that jointly estimates the number of endmembers, the endmembers itself, and their abundances, by making use of the Indian Buffet Process as a prior for the endmembers. Simulation results and experiments on real data demonstrate the effectiveness of the proposed algorithm, yielding results comparable with state-of-the-art methods while being able to reliably infer the number of endmembers. In scenarios with strong noise, where other algorithms provide only poor results, the proposed approach tends to overestimate the number of endmembers slightly. The additional endmembers, however, often simply represent noisy replicas of present endmembers and could easily be merged in a post-processing step

ADMM-Based Hyperspectral Unmixing Networks for Abundance and Endmember Estimation

Hyperspectral image (HSI) unmixing is an increasingly studied problem in various areas, including remote sensing. It has been tackled using both physical model-based approaches and more recently machine learning-based ones. In this article, we propose a new HSI unmixing algorithm combining both model- and learning-based techniques, based on algorithm unrolling approaches, delivering improved unmixing performance. Our approach unrolls the alternating direction method of multipliers (ADMMs) solver of a constrained sparse regression problem underlying a linear mixture model. We then propose a neural network structure for abundance estimation that can be trained using supervised learning techniques based on a new composite loss function. We also propose another neural network structure for blind unmixing that can be trained using unsupervised learning techniques. Our proposed networks are also shown to possess a lighter and richer structure containing less learnable parameters and more skip connections compared with other competing architectures. Extensive experiments show that the proposed methods can achieve much faster convergence and better performance even with a very small training dataset size when compared with other unmixing methods, such as model-inspired neural network for abundance estimation (MNN-AE), model-inspired neural network for blind unmixing (MNN-BU), unmixing using deep image prior (UnDIP), and endmember-guided unmixing network (EGU-Net)

Unsupervised clustering of hyperspectral images of brain tissues by hierarchical non-negative matrix factorization

International audienceHyperspectral images of high spatial and spectral resolutions are employed to perform the challenging task of brain tissue characterization and subsequent segmentation for visualization of in-vivo images. Each pixel is a high-dimensional spectrum. Working on the hypothesis of pure-pixels on account of high spectral resolution, we perform unsupervised clustering by hierarchical non-negative matrix factorization to identify the pure-pixel spectral signatures of blood, brain tissues, tumor and other materials. This subspace clustering was further used to train a random forest for subsequent classification of test set images constituent of in-vivo and ex-vivo images. Unsupervised hierarchical clustering helps visualize tissue structure in in-vivo test images and provides a inter-operative tool for surgeons. Furthermore the study also provides a preliminary study of the classification and sources of errors in the classification process

Automatic Denoising and Unmixing in Hyperspectral Image Processing

This thesis addresses two important aspects in hyperspectral image processing: automatic hyperspectral image denoising and unmixing. The first part of this thesis is devoted to a novel automatic optimized vector bilateral filter denoising algorithm, while the remainder concerns nonnegative matrix factorization with deterministic annealing for unsupervised unmixing in remote sensing hyperspectral images. The need for automatic hyperspectral image processing has been promoted by the development of potent hyperspectral systems, with hundreds of narrow contiguous bands, spanning the visible to the long wave infrared range of the electromagnetic spectrum. Due to the large volume of raw data generated by such sensors, automatic processing in the hyperspectral images processing chain is preferred to minimize human workload and achieve optimal result. Two of the mostly researched processing for such automatic effort are: hyperspectral image denoising, which is an important preprocessing step for almost all remote sensing tasks, and unsupervised unmixing, which decomposes the pixel spectra into a collection of endmember spectral signatures and their corresponding abundance fractions. Two new methodologies are introduced in this thesis to tackle the automatic processing problems described above. Vector bilateral filtering has been shown to provide good tradeoff between noise removal and edge degradation when applied to multispectral/hyperspectral image denoising. It has also been demonstrated to provide dynamic range enhancement of bands that have impaired signal to noise ratios. Typical vector bilateral filtering usage does not employ parameters that have been determined to satisfy optimality criteria. This thesis also introduces an approach for selection of the parameters of a vector bilateral filter through an optimization procedure rather than by ad hoc means. The approach is based on posing the filtering problem as one of nonlinear estimation and minimizing the Stein\u27s unbiased risk estimate (SURE) of this nonlinear estimator. Along the way, this thesis provides a plausibility argument with an analytical example as to why vector bilateral filtering outperforms band-wise 2D bilateral filtering in enhancing SNR. Experimental results show that the optimized vector bilateral filter provides improved denoising performance on multispectral images when compared to several other approaches. Non-negative matrix factorization (NMF) technique and its extensions were developed to find part based, linear representations of non-negative multivariate data. They have been shown to provide more interpretable results with realistic non-negative constrain in unsupervised learning applications such as hyperspectral imagery unmixing, image feature extraction, and data mining. This thesis extends the NMF method by incorporating deterministic annealing optimization procedure, which will help solve the non-convexity problem in NMF and provide a better choice of sparseness constrain. The approach is based on replacing the difficult non-convex optimization problem of NMF with an easier one by adding an auxiliary convex entropy constrain term and solving this first. Experiment results with hyperspectral unmixing application show that the proposed technique provides improved unmixing performance compared to other state-of-the-art methods