Given a set of mixed spectral (multispectral or hyperspectral) vectors, linear spectral mixture analysis, or linear unmixing, aims at estimating the number of reference substances, also called endmembers, their spectral signatures, and their abundance fractions. This paper presents a new method for unsupervised endmember extraction from hyperspectral data, termed vertex component analysis (VCA). The algorithm exploits two facts: (1) the endmembers are the vertices of a simplex and (2) the affine transformation of a simplex is also a simplex. In a series of experiments using simulated and real data, the VCA algorithm competes with state-of-the-art methods, with a computational complexity between one and two orders of magnitude lower than the best available method.

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Vertex component analysis: a fast algorithm to unmix hyperspectral data

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe.

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Histopathological Image Analysis: A Review

Hyperspectral imaging (HSI) is an emerging imaging modality for medical applications, especially in disease diagnosis and image-guided surgery. HSI acquires a three-dimensional dataset called hypercube, with two spatial dimensions and one spectral dimension. Spatially resolved spectral imaging obtained by HSI provides diagnostic information about the tissue physiology, morphology, and composition. This review paper presents an overview of the literature on medical hyperspectral imaging technology and its applications. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application.

https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-19/issue-1/010901/Medical-hyperspectral-imaging-a-review/10.1117/1.JBO.19.1.010901.pdf

Medical hyperspectral imaging: a review

Spectral mixture analysis provides an efficient mechanism for the interpretation and classification of remotely sensed multidimensional imagery. It aims to identify a set of reference signatures (also known as endmembers) that can be used to model the reflectance spectrum at each pixel of the original image. Thus, the modeling is carried out as a linear combination of a finite number of ground components. Although spectral mixture models have proved to be appropriate for the purpose of large hyperspectral dataset subpixel analysis, few methods are available in the literature for the extraction of appropriate endmembers in spectral unmixing. Most approaches have been designed from a spectroscopic viewpoint and, thus, tend to neglect the existing spatial correlation between pixels. This paper presents a new automated method that performs unsupervised pixel purity determination and endmember extraction from multidimensional datasets; this is achieved by using both spatial and spectral information in a combined manner. The method is based on mathematical morphology, a classic image processing technique that can be applied to the spectral domain while being able to keep its spatial characteristics. The proposed methodology is evaluated through a specifically designed framework that uses both simulated and real hyperspectral data.

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Spatial/spectral endmember extraction by multidimensional morphological operations

This paper presents an overview of methods that have been proposed for the analysis of breast cancer histopathology images. This research area has become particularly relevant with the advent of whole slide imaging (WSI) scanners, which can perform cost-effective and high-throughput histopathology slide digitization, and which aim at replacing the optical microscope as the primary tool used by pathologist. Breast cancer is the most prevalent form of cancers among women, and image analysis methods that target this disease have a huge potential to reduce the workload in a typical pathology lab and to improve the quality of the interpretation. This paper is meant as an introduction for nonexperts. It starts with an overview of the tissue preparation, staining and slide digitization processes followed by a discussion of the different image processing techniques and applications, ranging from analysis of tissue staining to computer-aided diagnosis, and prognosis of breast cancer patients.

Breast Cancer Histopathology Image Analysis: A Review

The authors have developed an automated feature detection/classification system, called GENetic Imagery Exploitation (GENIE), which has been designed to generate image processing pipelines for a variety of feature detection/classification tasks. GENIE is a hybrid evolutionary algorithm that addresses the general problem of finding features of interest in multispectral remotely-sensed images. The authors describe their system in detail together with experiments involving comparisons of GENIE with several conventional supervised classification techniques, for a number of classification tasks using multispectral remotely sensed imagery.

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Comparison of GENIE and conventional supervised classifiers for multispectral image feature extraction

We describe the implementation and performance of a genetic algorithm which generates image feature extraction algorithms for remote sensing applications. We describe our basis set of primitive image operators and present our chromosomal representation of a complete algorithm. Our initial application has been geospatial feature extraction using publicly available multi-spectral aerial-photography data sets. We present the preliminary results of our analysis of the efficiency of the classic genetic operations of crossover and mutation for our application, and discuss our choice of evolutionary control parameters. We exhibit some of our evolved algorithms, and discuss possible avenues for future progress.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

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Investigation of image feature extraction by a genetic algorithm

We present an analysis of the utility of multispectral versus standard RGB imagery for routine H&E stained histopathology images, in particular for pixel-level classification of nuclei Our multispectral imagery has 29 spectral bands, spaced 10 nm within the visual range of 420–700 nm It has been hypothesized that the additional spectral bands contain further information useful for classification as compared to the 3 standard bands of RGB imagery We present analyses of our data designed to test this hypothesis For classification using all available image bands, we find the best performance (equal tradeoff between detection rate and false alarm rate) is obtained from either the multispectral or our "ccd" RGB imagery, with an overall increase in performance of 079% compared to the next best performing image type For classification using single image bands, the single best multispectral band (in the red portion of the spectrum) gave a performance increase of 057%, compared to performance of the single best RGB band (red) Additionally, red bands had the highest coefficients/preference in our classifiers Principal components analysis of the multispectral imagery indicates only two significant image bands, which is not surprising given the presence of two stains Our results indicate that multispectral imagery for routine H&E stained histopathology provides minimal additional spectral information for a pixel-level nuclear classification task than would standard RGB imagery

https://www.cb.uu.se/~milan/histo/REFERENCES_final/Boucheron07.pdf

Utility of multispectral imaging for nuclear classification of routine clinical histopathology imagery.

We consider the problem of pixel-by-pixel classification of a multi- spectral image using supervised learning. Conventional spuervised classification techniques such as maximum likelihood classification and less conventional ones s uch as neural networks, typically base such classifications solely on the spectral components of each pixel. It is easy to see why: the color of a pixel provides a nice, bounded, fixed dimensional space in which these classifiers work well. It is often the case however, that spectral information alone is not sufficient to correctly classify a pixel. Maybe spatial neighborhood information is required as well. Or maybe the raw spectral components do not themselves make for easy classification, but some arithmetic combination of them would. In either of these cases we have the problem of selecting suitable spatial, spectral or spatio-spectral features that allow the classifier to do its job well. The number of all possible such features is extremely large. How can we select a suitable subset? We have developed GENIE, a hybrid learning system that combines a genetic algorithm that searches a space of image processing operations for a set that can produce suitable feature planes, and a more conventional classifier which uses those feature planes to output a final classification. In this paper we show that the use of a hybrid GA provides significant advantages over using either a GA alone or more conventional classification methods alone. We present results using high-resolution IKONOS data, looking for regions of burned forest and for roads.

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GENIE: a hybrid genetic algorithm for feature classification in multispectral images

The “pixel purity index” (PPI) algorithm proposed by Boardman, et al1 identifies potential endmember pixels in multispectral imagery. The algorithm generates a large number of “skewers” (unit vectors in random directions), and then computes the dot product of each skewer with each pixel. The PPI is incremented for those pixels associated with the extreme values of the dot products. A small number of pixels (a subset of those with the largest PPI values) are selected as “pure” and the rest of the pixels in the image are expressed as linear mixtures of these pure endmembers. This provides a convenient and physically-motivated decomposition of the image in terms of a relatively few components. We report on a variant of the PPI algorithm in which blocks of B skewers are considered at a time. Prom the computation of B dot products, one can produce a much larger set of “derived” dot products that are associated with skewers that are linear combinations of the original B skewers. Since the derived dot products involve only scalar operations, instead of full vector dot products, they can be very cheaply computed. We will also discuss a hardware implementation on a field programmable gate array (FPGA) processor both of the original PPI algorithm and of the block-skewer approach. We will furthermore discuss the use of fast PPI as a front-end to more sophisticated algorithms for selecting the actual endmembers.

/pdf/using-blocks-of-skewers-for-faster-computation-of-pixel-2gol5rxy36.pdf

Neal R. Harvey

Papers

Comparison of GENIE and conventional supervised classifiers for multispectral image feature extraction

Investigation of image feature extraction by a genetic algorithm

Utility of multispectral imaging for nuclear classification of routine clinical histopathology imagery.

GENIE: a hybrid genetic algorithm for feature classification in multispectral images

Using blocks of skewers for faster computation of pixel purity index