Image Analysis Software Tools Research Articles

Combining high-performance computing and networking for advanced 3-D cardiac imaging.

This paper deals with the integration of a powerful parallel computer-based image analysis and visualization system for cardiology into a hospital information system. Further services are remote access to the hospital Web server through an internet network. The visualization system includes dynamic three-dimensional representation of two types of medical images (e.g., magnetic resonance and nuclear medicine) as well as two images in the same modality (e.g., basal versus stress images). A series of software tools for quantitative image analysis developed for supporting diagnosis of cardiac disease are also available, including automated image segmentation and quantitative time evaluation of left ventricular volumes and related indices during cardiac cycle, myocardial mass, and myocardial perfusion indices. The system has been tested both at a specialized cardiologic center and for remote consultation in diagnosis of cardiac disease by using anatomical and perfusion magnetic resonance images.

High performance computing in biomedical imaging research

The Mayo Biomedical Imaging Resource (BIR) conducts research into and development of image analysis, visualization, and measurement capabilities and software tools for biomedical imaging applications. The design goal for these tools includes full interactivity, yet some tools are both compute bound and time sensitive. Therefore, effective use of these capabilities requires that they be executed on high performance computers. This paper provides an overview of the high performance computing activities in the BIR, including resources, algorithms and applications.

A simple computer based system to analyze Morris water maze trials on-line

The development of a system for the acquisition, analysis and storage of data from open-field water-maze procedures in which rats learn to escape from water onto a hidden platform is described. The use of an object-oriented programming language simplifies the programming of the application and provides scientists without formal training in computer programming the ability to create their own software application. The core hardware is an IBM-compatible AT 486 computer and a video capture board. The Microsoft Windows ® compatible software is written in G (LabVIEW) and presents the user a graphically based’ virtual instrument’ thus simulating functions of real instruments which can be interactively accessed. The graphical approach allows the programmer to make fast and simple adaptations of the software to suit the specific experimental problem. Image analysis software tools (Concept V.i) were integrated into this system which has been used successfully for over 2 years in our lab.

The merger of microscopy and advanced computing: A new frontier for the 21st century

Establishing and maintaining state-of-the-art national resources such as HVEM, IVEM and supercomputing centers involves considerable initial cost and continued support of staff with special skills and knowledge. The increased availability of high performance computing and communications offers scientists the potential for effective remote interactive use of such centralized, specialized, and expensive facilities. Anticipating improvements in computing and communications infrastructure, a collaborative computational environment, or “Collaboratory for Microscopic Digital Anatomy” (CMDA), is being developed that will provide a researcher at a remote site distributed interaction with unique instrumentation for the acquisition and manipulation of biological images. The prototype outlined in figure 1 was developed at the San Diego Microscopy and Imaging Resource. The CDMA integrates remote interactive acquisition and analysis of 2- and 3-dimensional electron microscopic data from state-of-the-art digital image acquisition systems such as a computer-controled IVEM. A software system has been developed that provides interactive control of image acquisition from the IVEM from a remote laboratory (and eventually any laboratory on the Internet). Sophisticated software tools for image analysis, visualization, and data management of these digital images are also under development. The system design will provide transparent distribution of tasks that require extensive computation to high performance computers accessible on the network. These tasks include the derivation of 3-dimensional structure using electron microscope tomography, automatic feature extraction for serial section reconstructions as well as manipulation and exploration of 3-dimensional biological datasets.