Histopathological image analysis : a review

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

Coupled non-parametric shape and moment-based inter-shape pose priors for multiple basal ganglia structure segmentation

This paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images. We present a set of 2D and 3D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy

Grid computing for the numerical reconstruction of digital holograms

Digital holography has the potential to greatly extend holography's applications and move it from the lab into the field: a single CCD or other solid-state sensor can capture any number of holograms while numerical reconstruction within a computer eliminates the need for chemical processing and readily allows further processing and visualisation of the holographic image. The steady increase in sensor pixel count and resolution leads to the possibilities of larger sample volumes and of higher spatial resolution sampling, enabling the practical use of digital off-axis holography. However this increase in pixel count also drives a corresponding expansion of the computational effort needed to numerically reconstruct such holograms to an extent where the reconstruction process for a single depth slice takes significantly longer than the capture process for each single hologram. Grid computing - a recent innovation in largescale distributed processing -provides a convenient means of harnessing significant computing resources in an ad-hoc fashion that might match the field deployment of a holographic instrument. In this paper we consider the computational needs of digital holography and discuss the deployment of numericals reconstruction software over an existing Grid testbed. The analysis of marine organisms is used as an exemplar for work flow and job execution of in-line digital holography

A multi-scale method to assess pesticide contamination risks in agricultural watersheds

The protection of water is now a major priority for environmental managers, especially around drinkingpumping stations. In view of the new challenges facing water agencies, we developed a method designedto support their public policy decision-making, at a variety of different spatial scales. In this paper, wepresent this new spatial method, using remote sensing and a GIS, designed to determine the contami-nation risk due to agricultural inputs, such as pesticides. The originality of this method lies in the useof a very detailed spatial object, the RSO (Reference Spatial Object), which can be aggregated to manyworking and managing scales. This has been achieved thanks to the pixel size of the remote sensing, witha grid resolution of 30 m × 30 m in our application.The method – called PHYTOPIXAL – is based on a combination of indicators relating to the environmen-tal vulnerability of the surface water environment (slope, soil type and distance to the stream) and theagricultural pressure (land use and practices of the farmers). The combination of these indicators for eachpixel provides the contamination risk. The scoring of variables was implemented according knowledgein literature and of experts.This method is used to target specific agricultural input transfer risks. The risk values are first calculatedfor each pixel. After this initial calculation, the data are then aggregated for decision makers, accordingto the most suitable levels of organisation. These data are based on an average value for the watershedareas.In this paper we detail an application of the method to an area in the hills of Southwest France. Weshow the pesticide contamination risk by in areas with different sized watersheds, ranging from 2 km2to 7000 km2, in which stream water is collected for consumption by humans and animals. The resultswere recently used by the regional water agency to determine the protection zoning for a large pumpingstation. Measures were then proposed to farmers with a view to improving their practices.The method can be extrapolated to different other areas to preserve or restore the surface water

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract