Novel two dimensional singular spectrum analysis for effective feature extraction and data classification in hyperspectral imaging

Feature extraction is of high importance for effective data classification in hyperspectral imaging (HSI). Considering the high correlation among band images, spectral-domain feature extraction is widely employed. For effective spatial information extraction, a 2-D extension to singular spectrum analysis (SSA), a recent technique for generic data mining and temporal signal analysis, is proposed. With 2D-SSA applied to HSI, each band image is decomposed into varying trend, oscillations and noise. Using the trend and selected oscillations as features, the reconstructed signal, with noise highly suppressed, becomes more robust and effective for data classification. Three publicly available data sets for HSI remote sensing data classification are used in our experiments. Comprehensive results using a support vector machine (SVM) classifier have quantitatively evaluated the efficacy of the proposed approach. Benchmarked with several state-of-the-art methods including 2-D empirical mode decomposition (2D-EMD), it is found that our proposed 2D-SSA approach generates the best results in most cases. Unlike 2D-EMD which requires sequential transforms to obtain detailed decomposition, 2D-SSA extracts all components simultaneously. As a result, the executive time in feature extraction can also be dramatically reduced. The superiority in terms of enhanced discrimination ability from 2D-SSA is further validated when a relatively weak classifier, k-nearest neighbor (k-NN), is used for data classification. In addition, the combination of 2D-SSA with 1D-PCA (2D-SSA-PCA) has generated the best results among several other approaches, which has demonstrated the great potential in combining 2D-SSA with other approaches for effective spatial-spectral feature extraction and dimension reduction in HSI

Exploring local spatial features in hyperspectral image

We propose a methodological framework to extract spatial features in hyperspectral imaging data and establish a link between these features and the spectral regions, capturing the observed structural patterns. The proposed approach consists of five main steps: i) two dimensional Stationary Wavelet Transform (2D-SWT) is applied to a hyperspectral data cube, decomposing each single-channel image with a selected wavelet filter up to the maximum decomposition level; ii) a grey-level co-occurrence matrix is calculated for every 2D-SWT image resulting from stage i); iii) distinctive spatial features are determined by computing morphological descriptors from each grey-level co-occurrence matrix; iv) the morphological descriptors are rearranged in a two dimensional data array; v) this data matrix is subjected to Principal Component Analysis (PCA) for exploring the variability of the aforementioned descriptors across spectral channels. As a result, groups of spectral wavelengths associated to specific spatial features can be pointed out yielding a better understanding and interpretation of the data. In principle, this information can also be further exploited, e.g. to improve the separation of pure spectral profiles in a multivariate curve resolution context

New algorithms for the analysis of live-cell images acquired in phase contrast microscopy

La détection et la caractérisation automatisée des cellules constituent un enjeu important dans de nombreux domaines de recherche tels que la cicatrisation, le développement de l'embryon et des cellules souches, l’immunologie, l’oncologie, l'ingénierie tissulaire et la découverte de nouveaux médicaments. Étudier le comportement cellulaire in vitro par imagerie des cellules vivantes et par le criblage à haut débit implique des milliers d'images et de vastes quantités de données. Des outils d'analyse automatisés reposant sur la vision numérique et les méthodes non-intrusives telles que la microscopie à contraste de phase (PCM) sont nécessaires. Comme les images PCM sont difficiles à analyser en raison du halo lumineux entourant les cellules et de la difficulté à distinguer les cellules individuelles, le but de ce projet était de développer des algorithmes de traitement d'image PCM dans Matlab® afin d’en tirer de l’information reliée à la morphologie cellulaire de manière automatisée. Pour développer ces algorithmes, des séries d’images de myoblastes acquises en PCM ont été générées, en faisant croître les cellules dans un milieu avec sérum bovin (SSM) ou dans un milieu sans sérum (SFM) sur plusieurs passages. La surface recouverte par les cellules a été estimée en utilisant un filtre de plage de valeurs, un seuil et une taille minimale de coupe afin d'examiner la cinétique de croissance cellulaire. Les résultats ont montré que les cellules avaient des taux de croissance similaires pour les deux milieux de culture, mais que celui-ci diminue de façon linéaire avec le nombre de passages. La méthode de transformée par ondelette continue combinée à l’analyse d'image multivariée (UWT-MIA) a été élaborée afin d’estimer la distribution de caractéristiques morphologiques des cellules (axe majeur, axe mineur, orientation et rondeur). Une analyse multivariée réalisée sur l’ensemble de la base de données (environ 1 million d’images PCM) a montré d'une manière quantitative que les myoblastes cultivés dans le milieu SFM étaient plus allongés et plus petits que ceux cultivés dans le milieu SSM. Les algorithmes développés grâce à ce projet pourraient être utilisés sur d'autres phénotypes cellulaires pour des applications de criblage à haut débit et de contrôle de cultures cellulaires.Automated cell detection and characterization is important in many research fields such as wound healing, embryo development, immune system studies, cancer research, parasite spreading, tissue engineering, stem cell research and drug research and testing. Studying in vitro cellular behavior via live-cell imaging and high-throughput screening involves thousands of images and vast amounts of data, and automated analysis tools relying on machine vision methods and non-intrusive methods such as phase contrast microscopy (PCM) are a necessity. However, there are still some challenges to overcome, since PCM images are difficult to analyze because of the bright halo surrounding the cells and blurry cell-cell boundaries when they are touching. The goal of this project was to develop image processing algorithms to analyze PCM images in an automated fashion, capable of processing large datasets of images to extract information related to cellular viability and morphology. To develop these algorithms, a large dataset of myoblasts images acquired in live-cell imaging (in PCM) was created, growing the cells in either a serum-supplemented (SSM) or a serum-free (SFM) medium over several passages. As a result, algorithms capable of computing the cell-covered surface and cellular morphological features were programmed in Matlab®. The cell-covered surface was estimated using a range filter, a threshold and a minimum cut size in order to look at the cellular growth kinetics. Results showed that the cells were growing at similar paces for both media, but their growth rate was decreasing linearly with passage number. The undecimated wavelet transform multivariate image analysis (UWT-MIA) method was developed, and was used to estimate cellular morphological features distributions (major axis, minor axis, orientation and roundness distributions) on a very large PCM image dataset using the Gabor continuous wavelet transform. Multivariate data analysis performed on the whole database (around 1 million PCM images) showed in a quantitative manner that myoblasts grown in SFM were more elongated and smaller than cells grown in SSM. The algorithms developed through this project could be used in the future on other cellular phenotypes for high-throughput screening and cell culture control applications

Novel Fourier Quadrature Transforms and Analytic Signal Representations for Nonlinear and Non-stationary Time Series Analysis

The Hilbert transform (HT) and associated Gabor analytic signal (GAS) representation are well-known and widely used mathematical formulations for modeling and analysis of signals in various applications. In this study, like the HT, to obtain quadrature component of a signal, we propose the novel discrete Fourier cosine quadrature transforms (FCQTs) and discrete Fourier sine quadrature transforms (FSQTs), designated as Fourier quadrature transforms (FQTs). Using these FQTs, we propose sixteen Fourier-Singh analytic signal (FSAS) representations with following properties: (1) real part of eight FSAS representations is the original signal and imaginary part is the FCQT of the real part, (2) imaginary part of eight FSAS representations is the original signal and real part is the FSQT of the real part, (3) like the GAS, Fourier spectrum of the all FSAS representations has only positive frequencies, however unlike the GAS, the real and imaginary parts of the proposed FSAS representations are not orthogonal to each other. The Fourier decomposition method (FDM) is an adaptive data analysis approach to decompose a signal into a set of small number of Fourier intrinsic band functions which are AM-FM components. This study also proposes a new formulation of the FDM using the discrete cosine transform (DCT) with the GAS and FSAS representations, and demonstrate its efficacy for improved time-frequency-energy representation and analysis of nonlinear and non-stationary time series.Comment: 22 pages, 13 figure

Large kernel spectral and spatial attention networks for hyperspectral image classification.

Currently, long-range spectral and spatial dependencies have been widely demonstrated to be essential for hyperspectral image (HSI) classification. Due to the transformer superior ability to exploit long-range representations, the transformer-based methods have exhibited enormous potential. However, existing transformer-based approaches still face two crucial issues that hinder the further performance promotion of HSI classification: 1) treating HSI as 1D sequences neglects spatial properties of HSI, 2) the dependence between spectral and spatial information is not fully considered. To tackle the above problems, a large kernel spectral-spatial attention network (LKSSAN) is proposed to capture the long-range 3D properties of HSI, which is inspired by the visual attention network (VAN). Specifically, a spectral-spatial attention module is first proposed to effectively exploit discriminative 3D spectral-spatial features while keeping the 3D structure of HSI. This module introduces the large kernel attention (LKA) and convolution feed-forward (CFF) to flexibly emphasize, model, and exploit the long-range 3D feature dependencies with lower computational pressure. Finally, the features from the spectral-spatial attention module are fed into the classification module for the optimization of 3D spectral-spatial representation. To verify the effectiveness of the proposed classification method, experiments are executed on four widely used HSI data sets. The experiments demonstrate that LKSSAN is indeed an effective way for long-range 3D feature extraction of HSI