Toward knowledge-based liver surgery: holistic information processing for surgical decision support.

PURPOSE: Malignant neoplasms of the liver are among the most frequent cancers worldwide. Given the diversity of options for liver cancer therapy, the choice of treatment depends on various parameters including patient condition, tumor size and location, liver function, and previous interventions. To address this issue, we present the first approach to treatment strategy planning based on holistic processing of patient-individual data, practical knowledge (i.e., case knowledge), and factual knowledge (e.g., clinical guidelines and studies). METHODS: The contributions of this paper are as follows: (1) a formalized dynamic patient model that incorporates all the heterogeneous data acquired for a specific patient in the whole course of disease treatment; (2) a concept for formalizing factual knowledge; and (3) a technical infrastructure that enables storing, accessing, and processing of heterogeneous data to support clinical decision making. RESULTS: Our patient model, which currently covers 602 patient-individual parameters, was successfully instantiated for 184 patients. It was sufficiently comprehensive to serve as the basis for the formalization of a total of 72 rules extracted from studies on patients with colorectal liver metastases or hepatocellular carcinoma. For a subset of 70 patients with these diagnoses, the system derived an average of [Formula: see text] assertions per patient. CONCLUSION: The proposed concept paves the way for holistic treatment strategy planning by enabling joint storing and processing of heterogeneous data from various information sources.

MITK-US: real-time ultrasound support within MITK.

PURPOSE: Intra-procedural acquisition of the patient anatomy is a key technique in the context of computer-assisted interventions (CAI). Ultrasound (US) offers major advantages as an interventional imaging modality because it is real time and low cost and does not expose the patient or physician to harmful radiation. To advance US-related research, the purpose of this paper was to develop and evaluate an open-source framework for US-based CAI applications. MATERIALS AND METHODS: We developed the open-source software module MITK-US for acquiring and processing US data as part of the well-known medical imaging interaction toolkit (MITK). To demonstrate its utility, we applied the module to implement a new concept for US-guided needle insertion. Performance of the US module was assessed by determining frame rate and latency for both a simple sample application and a more complex needle guidance system. RESULTS: MITK-US has successfully been used to implement both sample applications. Modern laptops achieve frame rates above 24 frames per second. Latency is measured to be approximately 250 ms or less. CONCLUSION: MITK-US can be considered a viable rapid prototyping environment for US-based CAI applications.

MITK diffusion imaging.

BACKGROUND: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets. OBJECTIVES: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field. METHODS: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITK-DI, are demonstrated using in-vivo datasets. RESULTS: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use installable application. CONCLUSIONS: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.

The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).

Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.

A quality-refinement process for medical imaging applications.

OBJECTIVES: To introduce and evaluate a process for refinement of software quality that is suitable to research groups. In order to avoid constraining researchers too much, the quality improvement process has to be designed carefully. The scope of this paper is to present and evaluate a process to advance quality aspects of existing research prototypes in order to make them ready for initial clinical studies. The proposed process is tailored for research environments and therefore more lightweight than traditional quality management processes. METHODS: Focus on quality criteria that are important at the given stage of the software life cycle. Usage of tools that automate aspects of the process is emphasized. To evaluate the additional effort that comes along with the process, it was exemplarily applied for eight prototypical software modules for medical image processing. RESULTS: The introduced process has been applied to improve the quality of all prototypes so that they could be successfully used in clinical studies. The quality refinement yielded an average of 13 person days of additional effort per project. Overall, 107 bugs were found and resolved by applying the process. CONCLUSIONS: Careful selection of quality criteria and the usage of automated process tools lead to a lightweight quality refinement process suitable for scientific research groups that can be applied to ensure a successful transfer of technical software prototypes into clinical research workflows.

Interactive segmentation framework of the Medical Imaging Interaction Toolkit.

Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the topic of interactive segmentation applications is rarely addressed by current toolkits and applications. In this paper, we present the extension of the Medical Imaging Interaction Toolkit (MITK) with a framework for the development of interactive applications for image segmentation. The framework provides a clear structure for the development of new applications and offers a plugin mechanism to easily extend existing applications with additional segmentation tools. In addition, the framework supports shape-based interpolation and multi-level undo/redo of modifications to binary images. To demonstrate the value of the framework, we also present a free, open-source application named InteractiveSegmentation for manual segmentation of medical images (including 3D+t), which is built based on the extended MITK framework. The application includes several features to effectively support manual segmentation, which are not found in comparable freely available applications. InteractiveSegmentation is fully developed and successfully and regularly used in several projects. Using the plugin mechanism, the application enables developers of new algorithms to begin algorithmic work more quickly.

Zero background yeast reporter plasmids.

UAS-less reporter plasmids are widespread and powerful tools for the identification and analysis of binding sites for transcriptional activators. The common reporter plasmids for the yeast Saccharomyces cerevisiae are multicopy (2mu) vectors with the CYC1 core promoter upstream of the lacZ gene. Insertion of putative or known activator binding sites upstream of the core promoter puts lacZ (beta-galactosidase) expression under the control of the corresponding activator. Although these constructs have proved to work well for most purposes, they have certain limitations: (1) they give significant and carbon-source-dependent lacZ background expression; (2) unlike most other yeast promoters, the CYC1 upstream region has a partially open chromatin structure with an accessible TATA box; (3) they use only a single, moderately sensitive reporter; and (4) the use of multicopy vectors can result in activator titration. Here, we introduce novel reporter plasmids based on the yeast MEL1 (alpha-galactosidase) gene that can overcome all of these limitations. It is also shown that background expression is due to fortuitous activator binding sites within the plasmid backbones that are insufficiently shielded from the core promoters in the common CYC1 reporter plasmids.

Neighborhood-based tobacco advertising targeting adolescents.

Adolescent tobacco use remains a serious problem, and adolescents may be particularly receptive to the glamorous images tobacco companies use in advertisements. A relatively new form of neighborhood-based outdoor advertising, the illuminated bus-stop-shelter billboard, was studied to determine tobacco companies' use of this medium. We hypothesized that in 2 distinct San Francisco, California, neighborhoods, 1 predominantly white and the other mostly Latino, we would find a predominance of tobacco advertising on these billboards in both neighborhoods, that tobacco advertisements would be more prevalent in the minority Latino neighborhood, and that tobacco advertising would target adolescents in both neighborhoods. Each bus-stop-shelter billboard advertisement in the study areas from April 1992 to March 1993 was recorded. The type and frequency of products advertised and qualitative content of tobacco advertisements were analyzed. Adolescents' possible exposure to these advertisements was noted. Our main outcome measures were the percentage of tobacco advertising, possible adolescent exposure to this advertising, and themes of the tobacco advertisements. About 10% of all bus-stop-shelter billboard advertisements in each area promoted tobacco use. Possible exposures to these advertisements were greater in the Latino neighborhood because of a greater adolescent population. Qualitative analyses of tobacco advertisements suggested that adolescents are the primary targets. We urge physicians and educators to explicitly address this form of tobacco advertising, and we urge a ban on neighborhood-based tobacco advertising.