By default ITK images use a contiguous memory model. This means pixel elements are stored in a single 1-D array, where each element is adjacent in memory to the previous element. However in some situations it is not desirable to use this memory model. This document describes three alternative memory models: slice contiguous, sparse, and single-bit binary images. Slice contiguous images are three-dimensional images, in which each slice is stored in a contiguous 1-D array, but the slices are not necessarily adjacent in memory. Slice contiguous images are well suited for interoperability with applications representing images using DICOM. Sparse images are n-dimensional images, in which each pixel is stored in a hash table data structure. This memory model is well suited for images with very large dimensions, but few pixels which are actually relevant. Single-bit binary images internally represent each pixel as a single-bit, in contrast to eight-bits required to represent a boolean. Single-bit binary images allow very compact representations for on-off masks. Source code, tests, and examples are provided to allow easy reproduction and use.

Alternative Memory Models for ITK Images

In the Digital Operating Room there is a need to support data streaming to create advanced integrated surgical assist systems. In this paper we propose a DICOM-based streaming mechanism which leverages the interoperability definitions offered by DICOM to offer a common interface to manage all kinds of streaming data sources, while allowing data and application-specific protocols and infrastructure for the actual data access. We have implemented the proposed solution within the ASTMA project and have shown that thanks to the flexibility in choosing an appropriate streaming protocol we can achieve the necessary streaming quality while transmitting the context information required to create valid DICOM instances. This approach ensures an early integration of streaming data with the rest of the imaging information providing for a simpler data workflow.

A DICOM-based streaming service for the Digital Operating Room

This paper presents an original role-based software architecture facilitating the flexible composition, configuration and collaboration of separated components in the field of computer assisted interventions. Roles, which can be seen as methods dynamically attached to objects, are embedded in components, to limit build level dependencies and improve flexibility. An appropriate component definition and composition language is proposed to declare softwares, without any specific initialization or glue code, this remaining a challenging issue in component oriented programming. The potential of this architecture is illustrated for a software coupling electromagnetic tracking with a robotized system dedicated to the physiological motion rejection in flexible endoscopy. This software consists in several independent components with are combined at runtime thanks to a concise XML-based declaration.

A role-based component architecture for computer assisted interventions: illustration for electromagnetic tracking and robotized motion rejection in flexible endoscopy

Various frameworks and toolkits have been proposed for rapid development of computer assisted intervention (CAI) software. In this paper, we investigate how the open-source 3D Slicer application framework can be used for this purpose. We defined common requirements for CAI software to evaluate and enhance 3D Slicer for interventional applications in general. 3D Slicer is found to be an appropriate end-user deployment environment for CAI software, as its built-in functions fulfill many requirements and missing functionalities can be conveniently added. We describe the implementation of a CAI software based on extending core 3D Slicer functions. Three enhancements are described in detail: the management of workflow, DICOM image transfer, and multiple views. The resulting software fulfills general CAI requirements and supports two different MRI-guided prostate biopsy systems (each with a different imaging mode, robotic manipulator and calibration method), thereby demonstrating the usability of Slicer for implementing different CAI applications.

A generic computer assisted intervention plug-in module for 3D Slicer with multiple device support

The rapid and ﬂexible visualization of large amounts of com- 
plex data has become a crucial part in medical image analysis. In re- 
cent years the Visualization Toolkit (VTK) has evolved as the de-facto 
standard for open-source medical data visualization. It features a clean 
design based on a data ﬂow paradigm, which the existing wrappers for 
VTK (Python, Tcl/Tk, Simulink) closely follow. This allows to elegantly 
model many types of algorithms, but presents a steep learning curve for 
beginners. In contrast to existing approaches we propose a framework 
for accessing VTK’s capabilities from within MATLAB, using a syntax 
which closely follows MATLAB’s graphics primitives. While providing 
users with the advanced, fast 3D visualization capabilities MATLAB 
does not provide, it is easy to learn while being ﬂexible enough to allow 
for complex plots, large amounts of data and combinations of visualiza- 
tions. The proposed framework will be made available as open source 
with detailed documentation and example data sets. 

MatVTK - 3D Visualization for Matlab

Developing both graphical and command-line user interfaces for image analysis algorithms requires considerable effort. Generally developers provide limited to very rudimentary user interface controls to their users. These image analysis algorithms can only meet their potential if they can be used easily and frequently by their intended users. Deployment of a large suite of such algorithms on multiple platforms requires that the software be stable and appropriately tested. 

We present a novel framework that allows for rapid development of image analysis algorithms along with graphical user interface controls. Additionally, our framework allows for simplified nightly testing of the algorithms to ensure stability and cross platform interoperability. It allows for development of complex algorithms by creating a custom pipeline where the output of an algorithm can serve as an input for another algorithm. All of the functionality is encapsulation into the object 
requiring no separate source code for user interfaces, testing or deployment. This makes our framework ideal for developing novel, stable and easy-to-use algorithms for computer assisted interventions (CAI). The framework has been deployed at the Magnetic Resonance Research Center at Yale University and has been released for public use. 

Unified framework for development, deployment and testing of image analysis algorithms

The Surgical Assistant Workstation (SAW) modular software framework provides integrated support
for robotic devices, imaging sensors, and a visualization pipeline for rapid prototyping of telesurgical
research systems. Subsystems of a telesurgical system, such as the master and slave robots and the visualization
engine, form a distributed environment that requires an efficient inter-process communication
(IPC) mechanism. This paper describes the extension of the component-based framework provided by
the cisst libraries, on which the SAW depends, from a multi-threaded (local) to a multi-process (networked)
environment. The current implementation uses the Internet Communication Engine (ICE) middleware
package, but the design does not depend on ICE and can accomodate other middleware choices.
A telesurgical robot system based on the da Vinci hardware platform is used as a test case, with a research
application that requires coordination between the left and right robot arms (a bimanual knot tying task).
Performance measurements on this platform indicate minimal overhead due to the networking.

A Surgical Assistant Workstation (SAW) Application for Teleoperated Surgical Robot System

An open standards based modular OR integration system was designed, which is modelled as component-based service-oriented architecture. Medical devices, IT hardware, and software are integrated as independent components and interconnected through a TCP/IP based Ethernet network. The integrated system facilitates service discovery, time synchronization, systems monitoring as well as component control and network administration. Each of the components exposes its semantic information about offered services as service description to peer components. The service description object is based on a generic model and contains all information about attributes, functions, streams as well as information on the used protocols that are required to access the services. An open standards based programming library for the rapid development of server/client components including example modules was developed. A prototype setup of the entire integrated OR system was realized within a demonstrator OR lab.

An integrated OR system based on open standards

Four-dimensional imaging is a necessary step in computer-assisted interventions (CAI) performed on moving surgical targets, such as those located within the beating heart or influenced by respiratory motion. Ultrasound (US) is often the best imaging modality for this application, as it provides good contrast and spatial resolution while remaining simple to integrate into the operating room. However, conventional 2D US imaging is often insufficient for preoperative planning and surgical guidance, real-time 3D ultrasound imaging using matrix array probes has a smaller field of view and lower spatial resolution, and 3D volumes created using 3D US reconstruction suffer from motion artifacts. As an alternative, gated 4D ultrasound reconstruction using a tracked 2D US probe is a promising technology. In this paper, we present SynchroGrab4D to the open-source community. SynchroGrab4D performs 3D and 4D US reconstruction in real-time while visualizing the output volume(s) within an OpenIGTLink-compliant CAI system, such as 3D Slicer. Also included are VTK classes that perform ECG-gating and that interface with several commercial tracking systems, as well as a 4D Imaging module in 3D Slicer. Our open-source imaging system can be used to collect the 4D image data required for computer-assisted surgical planning and intraoperative guidance for a variety of moving organs.

An open-source real-time ultrasound reconstruction system for four-dimensional imaging of moving organs

This document describes the role of DICOM as one major standard which will enable interoperability between systems used for surgical planning, intraoperative surgical assist systems and postoperative documentation. We first give an brief overview about DICOM and how it is constantly adapted and extended to cover the needs of new devices and application fields. We describe some of the recent additions which are relevant for image processing and intraoperative support in more detail, followed by a description of the current and future work of DICOM working group 24 "Surgery".