Petra Welter

Overview of the CLEF 2009 medical image annotation track

This paper describes the last round of the medical image annotation task in ImageCLEF 2009. After four years, we defined the task as a survey of all the past experience. Seven groups participated to the challenge submitting nineteen runs. They were asked to train their algorithms on 12677 images, labelled according to four different settings, and to classify 1733 images in the four annotation frameworks. The aim is to understand how each strategy answers to the increasing number of classes and to the unbalancing. A plain classification scheme using support vector machines and local descriptors outperformed the other methods.

Workflow management of content-based image retrieval for CAD support in PACS environments based on IHE.

PurposeContent-based image retrieval (CBIR) bears great potential for computer-aided diagnosis (CAD). However, current CBIR systems are not able to integrate with clinical workflow and PACS generally. One essential factor in this setting is scheduling. Applied and proved with modalities and the acquisition of images for a long time, we now establish scheduling with CBIR.MethodsOur workflow is based on the IHE integration profile ‘Post-Processing Workflow’ (PPW) and the use of a DICOM work list.ResultsWe configured dcm4chee PACS and its including IHE actors for the application of CBIR. In order to achieve a convenient interface for integrating arbitrary CBIR systems, we realized an adapter between the CBIR system and PACS. Our system architecture constitutes modular components communicating over standard protocols.ConclusionThe proposed workflow management system offers the possibility to embed CBIR conveniently into PACS environments. We achieve a chain of references that fills the information gap between acquisition and post-processing. Our approach takes into account the tight and solid organization of scheduled and performed tasks in clinical settings.

Content-based Image Retrieval Applied to Bone Age Assessment

Radiological bone age assessment is based on local image regions of interest (ROI), such as the epiphysis or the area of carpal bones. These are compared to a standardized reference and scores determining the skeletal maturity are calculated. For computer-aided diagnosis, automatic ROI extraction and analysis is done so far mainly by heuristic approaches. Due to high variations in the imaged biological material and differences in age, gender and ethnic origin, automatic analysis is difficult and frequently requires manual interactions. On the contrary, epiphyseal regions (eROIs) can be compared to previous cases with known age by content-based image retrieval (CBIR). This requires a sufficient number of cases with reliable positioning of the eROI centers. In this first approach to bone age assessment by CBIR, we conduct leaving-oneout experiments on 1,102 left hand radiographs and 15,428 metacarpal and phalangeal eROIs from the USC hand atlas. The similarity of the eROIs is assessed by cross-correlation of 16x16 scaled eROIs. The effects of the number of eROIs, two age computation methods as well as the number of considered CBIR references are analyzed. The best results yield an error rate of 1.16 years and a standard deviation of 0.85 years. As the appearance of the hand varies naturally by up to two years, these results clearly demonstrate the applicability of the CBIR approach for bone age estimation.

Generic integration of content-based image retrieval in computer-aided diagnosis

Content-based image retrieval (CBIR) offers approved benefits for computer-aided diagnosis (CAD), but is still not well established in radiological routine yet. An essential factor is the integration gap between CBIR systems and clinical information systems. The international initiative Integrating the Healthcare Enterprise (IHE) aims at improving interoperability of medical computer systems. We took into account deficiencies in IHE compliance of current picture archiving and communication systems (PACS), and developed an intermediate integration scheme based on the IHE post-processing workflow integration profile (PWF) adapted to CBIR in CAD. The Image Retrieval in Medical Applications (IRMA) framework was used to apply our integration scheme exemplarily, resulting in the application called IRMAcon. The novel IRMAcon scheme provides a generic, convenient and reliable integration of CBIR systems into clinical systems and workflows. Based on the IHE PWF and designed to grow at a pace with the IHE compliance of the particular PACS, it provides sustainability and fosters CBIR in CAD.

Bridging the integration gap between imaging and information systems: a uniform data concept for content-based image retrieval in computer-aided diagnosis

It is widely accepted that content-based image retrieval (CBIR) can be extremely useful for computer-aided diagnosis (CAD). However, CBIR has not been established in clinical practice yet. As a widely unattended gap of integration, a unified data concept for CBIR-based CAD results and reporting is lacking. Picture archiving and communication systems and the workflow of radiologists must be considered for successful data integration to be achieved. We suggest that CBIR systems applied to CAD should integrate their results in a picture archiving and communication systems environment such as Digital Imaging and Communications in Medicine (DICOM) structured reporting documents. A sample DICOM structured reporting template adaptable to CBIR and an appropriate integration scheme is presented. The proposed CBIR data concept may foster the promulgation of CBIR systems in clinical environments and, thereby, improve the diagnostic process.

Exemplary Design of a DICOM Structured Report Template for CBIR Integration into Radiological Routine

The large and continuously growing amount of medical image data demands access methods with regards to content rather than simple text-based queries. The potential benefits of content-based image retrieval (CBIR) systems for computer-aided diagnosis (CAD) are evident and have been approved. Still, CBIR is not a well-established part of daily routine of radiologists. We have already presented a concept of CBIR integration for the radiology workflow in accordance with the Integrating the Healthcare Enterprise (IHE) framework. The retrieval result is composed as a Digital Imaging and Communication in Medicine (DICOM) Structured Reporting (SR) document. The use of DICOM SR provides interchange with PACS archive and image viewer. It offers the possibility of further data mining and automatic interpretation of CBIR results. However, existing standard templates do not address the domain of CBIR. We present a design of a SR template customized for CBIR. Our approach is based on the DICOM standard templates and makes use of the mammography and chest CAD SR templates. Reuse of approved SR sub-trees promises a reliable design which is further adopted to the CBIR domain. We analyze the special CBIR requirements and integrate the new concept of similar images into our template. Our approach also includes the new concept of a set of selected images for defining the processed images for CBIR. A commonly accepted pre-defined template for the presentation and exchange of results in a standardized format promotes the widespread application of CBIR in radiological routine.

Towards a Repository for Standardized Medical Image and Signal Case Data Annotated with Ground Truth

Validation of medical signal and image processing systems requires quality-assured, representative and generally acknowledged databases accompanied by appropriate reference (ground truth) and clinical metadata, which are composed laboriously for each project and are not shared with the scientific community. In our vision, such data will be stored centrally in an open repository. We propose an architecture for a standardized case data and ground truth information repository supporting the evaluation and analysis of computer-aided diagnosis based on (a) the Reference Model for an Open Archival Information System (OAIS) provided by the NASA Consultative Committee for Space Data Systems (ISO 14721:2003), (b) the Dublin Core Metadata Initiative (DCMI) Element Set (ISO 15836:2009), (c) the Open Archive Initiative (OAI) Protocol for Metadata Harvesting, and (d) the Image Retrieval in Medical Applications (IRMA) framework. In our implementation, a portal bunches all of the functionalities that are needed for data submission and retrieval. The complete life cycle of the data (define, create, store, sustain, share, use, and improve) is managed. Sophisticated search tools make it easier to use the datasets, which may be merged from different providers. An integrated history record guarantees reproducibility. A standardized creation report is generated with a permanent digital object identifier. This creation report must be referenced by all of the data users. Peer-reviewed e-publishing of these reports will create a reputation for the data contributors and will form de-facto standards regarding image and signal datasets. Good practice guidelines for validation methodology complement the concept of the case repository. This procedure will increase the comparability of evaluation studies for medical signal and image processing methods and applications.

Bone age assessment by content-based image retrieval and case-based reasoning

Skeletal maturity is assessed visually by comparing hand radiographs to a standardized reference image atlas. Most common are the methods by Greulich & Pyle and Tanner & Whitehouse. For computer-aided diagnosis (CAD), local image regions of interest (ROI) such as the epiphysis or the carpal areas are extracted and evaluated. Heuristic approaches trying to automatically extract, measure and classify bones and distances between bones suffer from the high variability of biological material and the differences in bone development resulting from age, gender and ethnic origin. Content-based image retrieval (CBIR) provides a robust solution without delineating and measuring bones. In this work, epiphyseal ROIs (eROIS) of a hand radiograph are compared to previous cases with known age, mimicking a human observer. Leaving-one-out experiments are conducted on 1,102 left hand radiographs and 15,428 metacarpal and phalangeal eROIs from the publicly available USC hand atlas. The similarity of the eROIs is assessed by a combination of cross-correlation, image distortion model, and Tamura texture features, yielding a mean error rate of 0.97 years and a variance of below 0.63 years. Furthermore, we introduce a publicly available online-demonstration system, where queries on the USC dataset as well as on uploaded radiographs are performed for instant CAD. In future, we plan to evaluate physician with CBIR-CAD against physician without CBIR-CAD rather than physician vs. CBIR-CAD.

SubClass: classification of multidimensional noisy data using subspace clusters

Classification has been widely studied and successfully employed in various application domains. In multidimensional noisy settings, however, classification accuracy may be unsatisfactory. Locally irrelevant attributes often occlude class-relevant information. A global reduction to relevant attributes is often infeasible, as relevance of attributes is not necessarily a globally uniform property. In a current project with an airport scheduling software company, locally varying attributes in the data indicate whether flights will be on time, delayed or ahead of schedule. To detect locally relevant information, we propose combining classification with subspace clustering (SubClass). Subspace clustering aims at detecting clusters in arbitrary subspaces of the attributes. It has proved to work well in multidimensional and noisy domains. However, it does not utilize class label information and thus does not necessarily provide appropriate groupings for classification. We propose incorporating class label information into subspace search. As a result we obtain locally relevant attribute combinations for classification. We present the SubClass classifier that successfully exploits classifying subspace cluster information. Experiments on both synthetic and real world datasets demonstrate that classification accuracy is clearly improved for noisy multidimensional settings.

Combined DICOM and HL7 Viewer in Support of a Bridge from Content-Based Image Retrieval to Computer-Aided Diagnosis

Content-Based Image Retrieval (CBIR) is a field of rising interest for the application in Computer-Aided Diagnosis (CADx). Exploiting the visual information hidden in the images for retrieval, it facilitates the identification of similar past examinations, thereby providing a second opinion. Still, CBIR is not an integral part of a radiologist’s daily work. A comprehensive representation of CBIR results in a standard format utilizing established clinical infrastructure together with all referenced comparable examinations will support a bridge from CBIR to CADx. In this paper, we introduce the general IRMACON viewer, a system that represents results from CBIR systems encoded as a DICOM Structured Reporting document in a layout adjusted for CADx. IRMACON also allows the insight into identified similar examinations for convenient comparison by accessing patient’s information and diagnostic findings from the Hospital Information System (HIS) using HL7 messages. Our system is embedded into the clinical setting and the radiologist’s workflow. We applied the IRMACON viewer to the Image Retrieval in Medical Applications (IRMA) framework.