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".

The Role of DICOM for Modular Perioperative Surgical Assist Systems Design

We introduce a bio-inspired dynamic deformable (DET) model based on the equation of dynamics and including temporal smoothness constraints. The behaviour and characteristics of the dynamic DET model is studied in the context of the semi automatic spatio-temporal segmentation of the left ventricle myocardium in cine-MR images. The segmentation accuracy for endo/epicardium contours at end-diastole and end-systole, and as consequence the performance and limits of the current implementation, is evaluated in the context of the MICCAI LV Segmentation Challenge on a database of 15 multi-slice cine-MRI examinations.

Evaluation of the Dynamic Deformable Elastic Template model for the segmentation of the heart in MRI sequences

The motivation of the segmentation challenge is to quantitatively analyze global and regional cardiac function from cine magnetic resonance (MR) images, clinical parameters such as ejection fraction (EF), left ventricle myocardium mass (MM), and stroke volume (SV) are required. Calculations of these parameters depend upon accurate delineation of endocardial and epicardial contours of the left ventricle (LV). Manual delineation is time-consuming and tedious and has high inter-observer variability. Thus, fully automatic LV segmentation is desirable. 

The automatic segmentation of the LV in cine MR typically faces four challenges: 1) the overlap between the intensity distributions within the cardiac regions; 2) the lack of edge information; 3) the shape variability of the endocardial and epicardial contours across slices and phases; and 4) the inter-subject variability of these factors. A number of methods have been proposed for (semi-) automatic LV segmentation, including using a probability atlas [1], dynamic programming [2-3], fuzzy clustering [4], a deformable model [5], an active appearance model [6], a variational and level set [7-10], graph cuts [11-12] and an image-driven approach [13]. For a complete review of recent literature describing cardiac segmentation techniques, see [14]. Although the segmentation results have improved, accurate LV segmentation is still acknowledged as a difficult problem.

The goals of this contest are to compare LV segmentation methods by providing an evaluation system, and a database of images and expert contours. Comparing segmentation results across research studies can be difficult due to unspecified differences in the method or implementation of evaluation metrics. This contest will provide open-source code for contour evaluation. Furthermore, the database will provide a set of images such that confounding segmentation differences due to image quality or pathology could be eliminated.

Evaluation Framework for Algorithms Segmenting Short Axis Cardiac MRI.

We extended OpenIGTLink with following useful features; 1) AgentSocket class to capsulate socket initiation for smarter socket connection with try-catch implementation, 2) XmlMessage class to handle an XML text message. Using this extension, we will implement a data-logging DB that can relay the data to multiple clients.
This will impact the following 1) a pair of agent takes care of establishing, maintaining, terminating the communication channel, as well as attempting re-connection in case of network trouble, 2) modern error handling, 3) arbitrary format of data transfer by formatting an XML, including MRML data transmission via OpenIGTLink, 4) data logging by XML format. The work is yet in an early stage of implementation and a simple client example will be demonstrated.