On the Use of XML in Medical Imaging Web-Based Applications

The rapid growth of digital technology in medical fields over recent years has increased the need for applications able to manage patient medical records, imaging data, and chart information. Web-based applications are implemented with the purpose to link digital databases, storage and transmission protocols, management of large volumes of data and security concepts, allowing the possibility to read, analyze, and even diagnose remotely from the medical center where the information was acquired. The objective of this paper is to analyze the use of the Extensible Markup Language (XML) language in web-based applications that aid in diagnosis or treatment of patients, considering how this protocol allows indexing and exchanging the huge amount of information associated with each medical case. The purpose of this paper is to point out the main advantages and drawbacks of the XML technology in order to provide key ideas for future web-based applicationsPeer ReviewedPostprint (author's final draft

Αυτοματοποιημένη εξαγωγή μεταδεδομένων από πολλαπλές ιατρικές εικόνες μέσω τοπικού δικτύου

Η εκρηκτική αύξηση του αριθμού των βιοϊατρικών εικόνων τα τελευταία χρόνια απαιτεί νέες τεχνικές για τη διαχείριση των πληροφοριών που συλλέγονται. Πρόσθετες απεικονιστικές πληροφορίες, όπως οι παράμετροι σάρωσης και φιλτραρίσματος, αποθηκεύονται ως DICOM μεταδεδομένα, ενώ πρόσθετες πληροφορίες που σχετίζονται με τον ασθενή, όπως το ιατρικό ιστορικό, αποθηκεύονται συνήθως σε ένα σύστημα διαχείρισης βάσεων δεδομένων (DBMS). Τα συστήματα επικοινωνίας και αρχειοθέτησης εικόνων (PACS) αντιμετωπίζουν το ζήτημα της διαχείρισης των δεδομένων, αλλά αδυνατούν να πραγματοποιήσουν την αναζήτηση εικόνων και την εξαγωγή των αντίστοιχων μεταδεδομένων με βάση τις εγγραφές στο σύστημα DBMS. Ο στόχος αυτής της μελέτης είναι να αναπτυχθεί μια αυτοματοποιημένη μέθοδος για την αντιμετώπιση του προβλήματος της εξαγωγής μεταδεδομένων εικόνων από το σύστημα PACS μέσω τοπικού δικτύου. Σχεδιάστηκε μια εφαρμογή για απομακρυσμένο υπολογιστή, η οποία δημιουργεί και αποστέλλει αιτήματα στη βάση δεδομένων του απομακρυσμένου διακομιστή. Αναπτύχθηκαν αλγόριθμοι για την αναζήτηση των επιθυμητών αρχείων DICOM στον απομακρυσμένο διακομιστή PACS και την εξαγωγή των αντίστοιχων μεταδεδομένων. Η εφαρμογή επιτρέπει στους χρήστες να διαμορφώσουν αιτήματα και να αποθηκεύσουν τα αποτελέσματα σε ένα υπολογιστικό φύλλο εργασίας Microsoft Excel. Κατά τη διεκπεραίωση της μελέτης δόθηκε ιδιαίτερη έμφαση στην διασφάλιση των προσωπικών δεδομένων των ασθενών. Οι πληροφορίες που εξάγονται ταξινομούνται αυτόματα σε αρχείο Microsoft Excel και διατίθενται στον εξουσιοδοτημένο τελικό χρήστη σε ηλεκτρονική μορφή για περαιτέρω ανάλυση. Η ακεραιότητα και η αποτελεσματικότητα της μεθόδου αξιολογήθηκε μετά την αίτηση 171 αρχείων DICOM, ενώ η ακρίβεια των στοιχείων επιβεβαιώθηκε ποιοτικά.Explosive growth in the number of biomedical images in recent years requires new techniques to manage the information collected. Additional scan-related information, such as the acquisition parameters and filtration, is stored in DICOM metadata, while additional patient-related information, such as medical history or symptoms, is usually stored in a separated Database Management System (DBMS). Picture archiving and communication systems (PACS) can address the image data management issue, but PACS generally lack any methods for searching images and querying the metadata based on DBMS records. The objective of this study is to develop an automated method to address the problem of requiring biomedical image metadata from PACS over local network. A client application has been designed to make requests to the database of the remote server. Algorithms have been developed to query the remote PACS server for the specified DICOM files and extract all metadata. The application allows users to enter queries and store the results in a Microsoft Excel spreadsheet. This project has placed increasing emphasis on the security aspect of the patient’s personal data. The extracted information is automatically formatted and presented to the authorized end user as a Microsoft Excel file for data and trend analysis. The integrity and time efficacy of the method has been evaluated with a test sample of 171 DICOM files, while the accuracy of the data has been manually validated

Automated tracking of quantitative assessments of tumor Burden in clinical trials

There are two key challenges hindering effective use of quantitative assessment of imaging in cancer response assessment: 1) Radiologists usually describe the cancer lesions in imaging studies subjectively and sometimes ambiguously, and 2) it is difficult to repurpose imaging data, because lesion measurements are not recorded in a format that permits machine interpretation and interoperability. We have developed a freely available software platform on the basis of open standards, the electronic Physician Annotation Device (ePAD), to tackle these challenges in two ways. First, ePAD facilitates the radiologist in carrying out cancer lesion measurements as part of routine clinical trial image interpretation workflow. Second, ePAD records all image measurements and annotations in a data format that permits repurposing image data for analyses of alternative imaging biomarkers of treatment response. To determine the impact of ePAD on radiologist efficiency in quantitative assessment of imaging studies, a radiologist evaluated computed tomography (CT) imaging studies from 20 subjects having one baseline and three consecutive follow-up imaging studies with and without ePAD. The radiologist made measurements of target lesions in each imaging study using Response Evaluation Criteria in Solid Tumors 1.1 criteria, initially with the aid of ePAD, and then after a 30-day washout period, the exams were reread without ePAD. The mean total time required to review the images and summarize measurements of target lesions was 15% (P < .039) shorter using ePAD than without using this tool. In addition, it was possible to rapidly reanalyze the images to explore lesion cross-sectional area as an alternative imaging biomarker to linear measure.We conclude that ePAD appears promising to potentially improve reader efficiency for quantitative assessment of CT examinations, and it may enable discovery of future novel image-based biomarkers of cancer treatment response.National Cancer Institute, National Institutes of Health (grant U01CA142555)National Council for Scientific and Technological Development (CNPq grant 481837/2008-6

Scientific Digital Data Repositories: Needs and Challenges for Cancer Researchers

The purpose of this study is to understand the varied data needs of molecular level cancer researchers who use light, fluorescent, and electron microscopy to obtain knowledge about cancer on a molecular level. It explores what data tools a sample of researchers are currently using to preserve their data for future access, and the needs of these researchers for depositing their digital research data into digital repositories. Data from the researchers suggest that they understand the need to preserve their raw and compiled data in places outside their laboratory, but they have not fully embraced the idea of depositing it in a repository. This seems most likely due to them not fully understanding what repositories are and what they provide. To increase the use of repositories by this research community, repositories need to promote themselves better and to offer additional services that are specific for the needs of this community.Master of Science in Library Scienc

Uma proposta de arquitetura de alto desempenho para sistemas PACS baseada em extensões de banco de dados

Orientador : Prof. Dr. Aldo Von WangenheimTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 25/07/2014Inclui referênciasResumo: O uso de imagens digitais no processo de diagnóstico médico é observável em diferentes escalas e cenários de aplicação, tendo evoluído em termos de volume de dados adquiridos e número de modalidades de exame atendidas. A organização desse conteúdo digital, comumente representado por conjuntos de imagens no pa-drão DICOM (Digital Imaging and Communications in Medicine), costuma ser dele-gada a sistemas PACS (Picture Archiving and Communication System) baseados na agregação de componentes heterogêneos de hardware e software. Parte desses componentes interage de forma a compor a camada de armazenamento do PACS, responsável pela persistência de toda e qualquer imagem digital que, em algum momento, foi adquirida ou visualizada/manipulada via sistema. Apesar de emprega-rem recursos altamente especializados como SGBDs (Sistemas Gerenciadores de Banco de Dados), as camadas de armazenamento PACS atuais são visualizadas e utilizadas como simples repositórios de dados, assumindo um comportamento pas-sivo (ou seja, sem a agregação de regras de negócio) quando comparadas a outros componentes do sistema. Neste trabalho, propõe-se uma nova arquitetura PACS simplificada baseada em alterações na sua camada de armazenamento. As alterações previstas baseiam-se na troca do perfil passivo assumido atualmente por essa camada por um perfil ativo, utilizando-se de recursos de extensibilidade e de distribuição de dados (hoje não empregados) disponibilizados por seus componentes. A arquitetura proposta concentra-se na comunicação e no armazenamento de dados, utilizando-se de ex-tensões de SGBDs e de estruturas heterogêneas para armazenamento de dados convencionais e não convencionais, provendo alto desempenho em termos de es-calabilidade, suporte a grandes volumes de conteúdo e processamento descentrali-zado de consultas. Estruturalmente, a arquitetura proposta é formada por um con-junto de módulos projetados de forma a explorar as opções de extensibilidade pre-sentes em SGBDs, incorporando características e funcionalidades originalmente dis-tribuídas entre outros componentes do PACS (na forma de regras de negócio). Em nível de protótipo, resultados obtidos a partir de experimentos indicam a viabilidade de uso da arquitetura proposta, explicitando ganhos de desempenho na pesquisa de metadados e na recuperação de imagens DICOM quando comparados a arquiteturas PACS convencionais. A flexibilidade da proposta quanto à adoção de tecnologias de armazenamento heterogêneas também é avaliada positivamente, permitindo estender a camada de armazenamento PACS em termos de escalabili-dade, poder de processamento, tolerância a falhas e representação de conteúdo. Palavras-chave: PACS, DICOM, SGBD, extensibilidade, alto desempenho.Abstract: The use of digital images on medical diagnosis is observable in a number of application scenarios and in different scales, growing in terms of volume of data and contemplated medical specialties. To organize this digital content composed by image datasets in DICOM (Digital Imaging and Communications in Medicine), it is usual to adopt PACS (Picture Archiving and Communication System), an architecture built as an aggregation of hardware and software components. Some of these components compose the so-called PACS's storage layer, responsible for the persistence of every digital image acquired or visualized/manipulated through the system. Despite their high-specialized components (e.g., DBMS - Database Management System), PACS storage layers used today are visualized as simple data repositories, assuming a passive role (i.e., without the implementation of business rules) when compared to other components. In this work, a simplified, new architecture is proposed for PACS, based in modifications on its storage layer. The modifications are based in the replacement of the current passive role by an active one, using extensibility and data distribution resources available on its components. The proposed architecture focuses on communication and data storage, using DBMS extensions and heterogeneous structures for the storage of conventional and non-conventional data, providing high-performance in terms of scalability, support to large volumes of data and decentralized query processing. Structurally, the proposed architecture is composed by a set of modules designed to explore extensibility options available in DBMSs, incorporating characteristics and functionalities originally distributed as business rules among other components of PACS. At prototype level, results obtained through experiments indicate the viability of the proposal, making explicit the performance gains in the search for metadata and image retrieval when compared to conventional PACS architectures. The flexibility of the proposal regarding the adoption of heterogeneous storage technologies is also positively evaluated, allowing the extension of the PACS storage layer in terms of scalability, processing power, fault tolerance and content representation. Keywords: PACS, DICOM, DBMS, extensibility, High-Performance Computing