NeuroTerrain--a client-server system for browsing 3D biomedical image data sets

Abstract

Background: Three dimensional biomedical image sets are becoming ubiquitous, along with the canonical atlases providing the necessary spatial context for analysis. To make full use of these 3D image sets, one must be able to present views for 2D display, either surface renderings or 2D cross-sections through the data. Typical display software is limited to presentations along one of the three orthogonal anatomical axes (coronal, horizontal, or sagittal). However, data sets precisely oriented along the major axes are rare. To make fullest use of these datasets, one must reasonably match the atlas' orientation; this involves resampling the atlas in planes matched to the data set. Traditionally, this requires the atlas and browser reside on the user's desktop; unfortunately, in addition to being monolithic programs, these tools often require substantial local resources. In this article, we describe a network-capable, client-server framework to slice and visualize 3D atlases at off-axis angles, along with an open client architecture and development kit to support integration into complex data analysis environments.

Results: Here we describe the basic architecture of a client-server 3D visualization system, consisting of a thin Java client built on a development kit, and a computationally robust, high-performance server written in ANSI C++. The Java client components (NetOStat) support arbitrary-angle viewing and run on readily available desktop computers running Mac OS X, Windows XP, or Linux as a downloadable Java Application. Using the NeuroTerrain Software Development Kit (NT-SDK), sophisticated atlas browsing can be added to any Java-compatible application requiring as little as 50 lines of Java glue code, thus making it eminently re-useable and much more accessible to programmers building more complex, biomedical data analysis tools. The NT-SDK separates the interactive GUI components from the server control and monitoring, so as to support development of non-interactive applications. The server implementation takes full advantage of data center's high-performance hardware, where it can be co-localized with centrally-located, 3D dataset repositories, extending access to the researcher community throughout the Internet.

Conclusion: The combination of an optimized server and modular, platform-independent client provides an ideal environment for viewing complex 3D biomedical datasets, taking full advantage of high-performance servers to prepare images and subsets of associated meta-data for viewing, as well as the graphical capabilities in Java to actually display the data.

Figure 1

NeuroTerrain Server Functional components. The NeuroTerrain Server is composed of several distinct software modules which inter-relate in a precise way, a subset of which interact directly with a connected client. Please see Main Server Modules section of the text for a more complete description of these separate components.

Figure 2

NT-SDK User Interface components. (a) Via the Virtual Knife wireframe, the user can continuously adjust the cross-sectional slice position through the current 3D atlas volume(s) mounted on the server. By dragging the mouse left or right over the wireframe, the knife is displaced along the currently selected anatomical axis. The Knife Position indicates the cross-section location in terms of the current linear displacement (Δ) along the slice axis, and the rotational angles about the standard X, Y, and Z cartesian axes. The knife can also be minimally nudged via the left and right arrow buttons. The Motion buttons specify whether mouse movement causes translation about this axis, or rotation about the X, Y or Z cartesian axes. (b) These SV control panel tool buttons alter the state of the data in the viewer. The Axis specifies whether the knife is adjusted along the coronal, sagittal, or horizontal cutting axes. The VOI buttons enable the investigator to toggle VOI viewing on/off and to choose the segmented regions to view. The Zoom button adjusts the scale of the current atlas view from 0.1× to 10.0×. When zoomed in, a crop window is imposed to limit network data transmission, which can be adjusted by dragging on the grayscale view or centered via the Center Crop button. The Mark buttons are used to save a specific view cross-section position for recall, and enable the investigator to respectively save, open, and clear the marks menu. The Save Image buttons respectively save the current slice view to a file or provide a means to resample an extended portion of the data set under view. (c) This full view of the NtAS Client (NetOStat), shows the relation of the controls in b to the gray-scale cross-sectional atlas view. At the bottom of this frame are controls to view the current image scale and cursor location, when the mouse cursor is placed over the atlas image. Mouse over location can be translated into stereotaxic coordinates when coordinate transformation matrices are available, as they are for the NT Adult Mouse Atlas.

Figure 3

Atlas VOI selection. The VOI selection button sends a request to the server to obtain a list of VOIs for the currently loaded 3D atlas data set. This listing of VOIs is presented to the researcher on the above form (a), from which she can selectively activate specific VOIs for viewing superimposed on the atlas view. (b).