How to Optimize Connection Between PACS and Clinical Data Warehouse: A Web Service Approach Based on Full Metadata Integration.

Clinical image data analysis is an active area of research. Integrating such data in a Clinical Data Warehouse (CDW) implies to unlock the PACS and RIS and to address interoperability and semantics issues. Based on specific functional and technical requirements, our goal was to propose a web service (I4DW) that allows users to query and access pixel data from a CDW by fully integrating and indexing imaging metadata. Here, we present the technical implementation of this workflow as well as the evaluation we carried out using a prostate cancer cohort use case. The query mechanism relies on a Dicom metadata hierarchy dynamically generated during the ETL Process. We evaluated the Dicom data transfer performance of I4DW, and found mean retrieval times of 5.94 seconds and 0.9 seconds to retrieve a complete DICOM series from the PACS and all metadata of a series. We could retrieve all patients and imaging tests of the prostate cancer cohort with a precision of 0.95 and a recall of 1. By leveraging the CMOVE method, our approach based on the Dicom protocol is scalable and domain-neutral. Future improvement will focus on performance optimization and de identification.

Surgical data science - from concepts toward clinical translation.

Recent developments in data science in general and machine learning in particular have transformed the way experts envision the future of surgery. Surgical Data Science (SDS) is a new research field that aims to improve the quality of interventional healthcare through the capture, organization, analysis and modeling of data. While an increasing number of data-driven approaches and clinical applications have been studied in the fields of radiological and clinical data science, translational success stories are still lacking in surgery. In this publication, we shed light on the underlying reasons and provide a roadmap for future advances in the field. Based on an international workshop involving leading researchers in the field of SDS, we review current practice, key achievements and initiatives as well as available standards and tools for a number of topics relevant to the field, namely (1) infrastructure for data acquisition, storage and access in the presence of regulatory constraints, (2) data annotation and sharing and (3) data analytics. We further complement this technical perspective with (4) a review of currently available SDS products and the translational progress from academia and (5) a roadmap for faster clinical translation and exploitation of the full potential of SDS, based on an international multi-round Delphi process.

Explaining a model predicting quality of surgical practice: a first presentation to and review by clinical experts.

PURPOSE: Surgical Data Science (SDS) is an emerging research domain offering data-driven answers to challenges encountered by clinicians during training and practice. We previously developed a framework to assess quality of practice based on two aspects: exposure of the surgical scene (ESS) and the surgeon's profile of practice (SPP). Here, we wished to investigate the clinical relevance of the parameters learned by this model by (1) interpreting these parameters and identifying associated representative video samples and (2) presenting this information to surgeons in the form of a video-enhanced questionnaire. To our knowledge, this is the first approach in the field of SDS for laparoscopy linking the choices made by a machine learning model predicting surgical quality to clinical expertise. METHOD: Spatial features and quality of practice scores extracted from labeled and segmented frames in 30 laparoscopic videos were used to predict the ESS and the SPP. The relationships between the inputs and outputs of the model were then analyzed and translated into meaningful sentences (statements, e.g., "To optimize the ESS, it is very important to correctly handle the spleen"). Representative video clips illustrating these statements were semi-automatically identified. Eleven statements and video clips were used in a survey presented to six experienced digestive surgeons to gather their opinions on the algorithmic analyses. RESULTS: All but one of the surgeons agreed with the proposed questionnaire overall. On average, surgeons agreed with 7/11 statements. CONCLUSION: This proof-of-concept study provides preliminary validation of our model which has a high potential for use to analyze and understand surgical practices.

A multicentric IT platform for storage and sharing of imaging-based radiation dosimetric data.

PURPOSE: The MEDIRAD project is about the effects of low radiation dose in the context of medical procedures. The goal of the work is to develop an informatics service that will provide the researchers of the MEDIRAD project with a platform to share acquired images, along with the associated dosimetric data pertaining to the radiation resulting from the procedure. METHODS: The authors designed a system architecture to manage image data and dosimetric data in an integrated way. DICOM and non-DICOM data are stored in separated repositories, and the link between the two is provided through a semantic database, i.e., a database whose information schema in aligned with an ontology. RESULTS: The system currently supports CT, PET, SPECT, and NM images as well as dose reports. Currently, two workflows for non-DICOM data generated from dosimetric calculations have been taken into account, one concerning Monte Carlo-based calculation of organ doses in Chest CT, and the other estimation of doses in nontarget organs in 131I targeted radionuclide therapy of the thyroid. CONCLUSION: The system is currently deployed, thus providing access to image and related dosimetric data to all MEDIRAD users. The software was designed in such a way that it can be reused to support similar needs in other projects.

A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging.

Medical ionizing radiation procedures and especially medical imaging are a non negligible source of exposure to patients. Whereas the biological effects of high absorbed doses are relatively well known, the effects of low absorbed doses are still debated. This work presents the development of a computer platform called Image and Radiation Dose BioBank (IRDBB) to manage research data produced in the context of the MEDIRAD project, a European project focusing on research on low doses in the context of medical procedures. More precisely, the paper describes a semantic database linking dosimetric data (such as absorbed doses to organs) to the images corresponding to X-rays exposure (such as CT images) or scintigraphic images (such as SPECT or PET images) that allow measuring the distribution of a radiopharmaceutical. The main contributions of this work are: 1) the implementation of the semantic database of the IRDBB system and 2) an ontology called OntoMEDIRAD covering the domain of discourse involved in MEDIRAD research data, especially many concepts from the DICOM standard modelled according to a realist approach.

Predicting the quality of surgical exposure using spatial and procedural features from laparoscopic videos.

PURPOSE : Evaluating the quality of surgical procedures is a major concern in minimally invasive surgeries. We propose a bottom-up approach based on the study of Sleeve Gastrectomy procedures, for which we analyze what we assume to be an important indicator of the surgical expertise: the exposure of the surgical scene. We first aim at predicting this indicator with features extracted from the laparoscopic video feed, and second to analyze how the extracted features describing the surgical practice influence this indicator. METHOD : Twenty-nine patients underwent Sleeve Gastrectomy performed by two confirmed surgeons in a monocentric study. Features were extracted from spatial and procedural annotations of the videos, and an expert surgeon evaluated the quality of the surgical exposure at specific instants. The features were used as input of a classifier (linear discriminant analysis followed by a support vector machine) to predict the expertise indicator. Features selected in different configurations of the algorithm were compared to understand their relationships with the surgical exposure and the surgeon's practice. RESULTS : The optimized algorithm giving the best performance used spatial features as input ([Formula: see text]). It also predicted equally the two classes of the indicator, despite their strong imbalance. Analyzing the selection of input features in the algorithm allowed a comparison of different configurations of the algorithm and showed a link between the surgical exposure and the surgeon's practice. CONCLUSION : This preliminary study validates that a prediction of the surgical exposure from spatial features is possible. The analysis of the clusters of feature selected by the algorithm also shows encouraging results and potential clinical interpretations.

Learning procedural skills with a virtual reality simulator: An acceptability study.

BACKGROUND: Virtual Reality (VR) simulation has recently been developed and has improved surgical training. Most VR simulators focus on learning technical skills and few on procedural skills. Studies that evaluated VR simulators focused on feasibility, reliability or easiness of use, but few of them used a specific acceptability measurement tool. OBJECTIVES: The aim of the study was to assess acceptability and usability of a new VR simulator for procedural skill training among scrub nurses, based on the Unified Theory of Acceptance and Use of Technology (UTAUT) model. PARTICIPANTS: The simulator training system was tested with a convenience sample of 16 non-expert users and 13 expert scrub nurses from the neurosurgery department of a French University Hospital. METHODS: The scenario was designed to train scrub nurses in the preparation of the instrumentation table for a craniotomy in the operating room (OR). RESULTS: Acceptability of the VR simulator was demonstrated with no significant difference between expert scrub nurses and non-experts. There was no effect of age, gender or expertise. Workload, immersion and simulator sickness were also rated equally by all participants. Most participants stressed its pedagogical interest, fun and realism, but some of them also regretted its lack of visual comfort. CONCLUSION: This VR simulator designed to teach surgical procedures can be widely used as a tool in initial or vocational training.

Toward a standard ontology of surgical process models.

PURPOSE: The development of common ontologies has recently been identified as one of the key challenges in the emerging field of surgical data science (SDS). However, past and existing initiatives in the domain of surgery have mainly been focussing on individual groups and failed to achieve widespread international acceptance by the research community. To address this challenge, the authors of this paper launched a European initiative-OntoSPM Collaborative Action-with the goal of establishing a framework for joint development of ontologies in the field of SDS. This manuscript summarizes the goals and the current status of the international initiative. METHODS: A workshop was organized in 2016, gathering the main European research groups having experience in developing and using ontologies in this domain. It led to the conclusion that a common ontology for surgical process models (SPM) was absolutely needed, and that the existing OntoSPM ontology could provide a good starting point toward the collaborative design and promotion of common, standard ontologies on SPM. RESULTS: The workshop led to the OntoSPM Collaborative Action-launched in mid-2016-with the objective to develop, maintain and promote the use of common ontologies of SPM relevant to the whole domain of SDS. The fundamental concept, the architecture, the management and curation of the common ontology have been established, making it ready for wider public use. CONCLUSION: The OntoSPM Collaborative Action has been in operation for 24 months, with a growing dedicated membership. Its main result is a modular ontology, undergoing constant updates and extensions, based on the experts' suggestions. It remains an open collaborative action, which always welcomes new contributors and applications.

Relevance of health level 7 clinical document architecture and integrating the healthcare enterprise cross-enterprise document sharing profile for managing chronic wounds in a telemedicine context.

The number of patients with complications associated with chronic diseases increases with the ageing population. In particular, complex chronic wounds raise the re-admission rate in hospitals. In this context, the implementation of a telemedicine application in Basse-Normandie, France, contributes to reduce hospital stays and transport. This application requires a new collaboration among general practitioners, private duty nurses and the hospital staff. However, the main constraint mentioned by the users of this system is the lack of interoperability between the information system of this application and various partners' information systems. To improve medical data exchanges, the authors propose a new implementation based on the introduction of interoperable clinical documents and a digital document repository for managing the sharing of the documents between the telemedicine application users. They then show that this technical solution is suitable for any telemedicine application and any document sharing system in a healthcare facility or network.

Synthesis and Simulation of Surgical Process Models.

Virtual Reality for surgical training is mainly focused on technical surgical skills. We work on providing a novel approach to the use of Virtual Reality focusing on the procedural aspects. Our system relies on a specific work-flow generating a model of the procedure from real case surgery observation in the operating room. This article presents the different technologies created in the context of our project and their relations as other components of our workflow.

Biomedical imaging ontologies: A survey and proposal for future work.

BACKGROUND: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as "cell" or "image" or "tissue" or "microscope") that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical definitions thereby also supporting reasoning over the tagged data. AIM: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. RESULTS AND CONCLUSIONS: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.

LapOntoSPM: an ontology for laparoscopic surgeries and its application to surgical phase recognition.

PURPOSE: The rise of intraoperative information threatens to outpace our abilities to process it. Context-aware systems, filtering information to automatically adapt to the current needs of the surgeon, are necessary to fully profit from computerized surgery. To attain context awareness, representation of medical knowledge is crucial. However, most existing systems do not represent knowledge in a reusable way, hindering also reuse of data. Our purpose is therefore to make our computational models of medical knowledge sharable, extensible and interoperational with established knowledge representations in the form of the LapOntoSPM ontology. To show its usefulness, we apply it to situation interpretation, i.e., the recognition of surgical phases based on surgical activities. METHODS: Considering best practices in ontology engineering and building on our ontology for laparoscopy, we formalized the workflow of laparoscopic adrenalectomies, cholecystectomies and pancreatic resections in the framework of OntoSPM, a new standard for surgical process models. Furthermore, we provide a rule-based situation interpretation algorithm based on SQWRL to recognize surgical phases using the ontology. RESULTS: The system was evaluated on ground-truth data from 19 manually annotated surgeries. The aim was to show that the phase recognition capabilities are equal to a specialized solution. The recognition rates of the new system were equal to the specialized one. However, the time needed to interpret a situation rose from 0.5 to 1.8 s on average which is still viable for practical application. CONCLUSION: We successfully integrated medical knowledge for laparoscopic surgeries into OntoSPM, facilitating knowledge and data sharing. This is especially important for reproducibility of results and unbiased comparison of recognition algorithms. The associated recognition algorithm was adapted to the new representation without any loss of classification power. The work is an important step to standardized knowledge and data representation in the field on context awareness and thus toward unified benchmark data sets.

Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study.

Different non-invasive neuroimaging modalities and multi-level analysis of human connectomics datasets yield a great amount of heterogeneous data which are hard to integrate into an unified representation. Biomedical ontologies can provide a suitable integrative framework for domain knowledge as well as a tool to facilitate information retrieval, data sharing and data comparisons across scales, modalities and species. Especially, it is urgently needed to fill the gap between neurobiology and in vivo human connectomics in order to better take into account the reality highlighted in Magnetic Resonance Imaging (MRI) and relate it to existing brain knowledge. The aim of this study was to create a neuroanatomical ontology, called "Human Connectomics Ontology" (HCO), in order to represent macroscopic gray matter regions connected with fiber bundles assessed by diffusion tractography and to annotate MRI connectomics datasets acquired in the living human brain. First a neuroanatomical "view" called NEURO-DL-FMA was extracted from the reference ontology Foundational Model of Anatomy (FMA) in order to construct a gross anatomy ontology of the brain. HCO extends NEURO-DL-FMA by introducing entities (such as "MR_Node" and "MR_Route") and object properties (such as "tracto_connects") pertaining to MR connectivity. The Web Ontology Language Description Logics (OWL DL) formalism was used in order to enable reasoning with common reasoning engines. Moreover, an experimental work was achieved in order to demonstrate how the HCO could be effectively used to address complex queries concerning in vivo MRI connectomics datasets. Indeed, neuroimaging datasets of five healthy subjects were annotated with terms of the HCO and a multi-level analysis of the connectivity patterns assessed by diffusion tractography of the right medial Brodmann Area 6 was achieved using a set of queries. This approach can facilitate comparison of data across scales, modalities and species.

A multilayer ontology of instruments for neurological, behavioral and cognitive assessments.

Advances in neuroscience are underpinned by large, multicenter studies and a mass of heterogeneous datasets. When investigating the relationships between brain anatomy and brain functions under normal and pathological conditions, measurements obtained from a broad range of brain imaging techniques are correlated with the information on each subject's neurologic states, cognitive assessments and behavioral scores derived from questionnaires and tests. The development of ontologies in neuroscience appears to be a valuable way of gathering and handling properly these heterogeneous data - particularly through the use of federated architectures. We recently proposed a multilayer ontology for sharing brain images and regions of interest in neuroimaging. Here, we report on an extension of this ontology to the representation of instruments used to assess brain and cognitive functions and behavior in humans. This extension consists of a 'core' ontology that accounts for the properties shared by all instruments supplemented by 'domain' ontologies that conceptualize standard instruments. We also specify how this core ontology has been refined to build domain ontologies dedicated to widely used instruments and how various scores used in the neurosciences are represented. Lastly, we discuss our design choices, the ontology's limitations and planned extensions aimed at querying and reasoning across distributed data sources.

OntoVIP: an ontology for the annotation of object models used for medical image simulation.

This paper describes the creation of a comprehensive conceptualization of object models used in medical image simulation, suitable for major imaging modalities and simulators. The goal is to create an application ontology that can be used to annotate the models in a repository integrated in the Virtual Imaging Platform (VIP), to facilitate their sharing and reuse. Annotations make the anatomical, physiological and pathophysiological content of the object models explicit. In such an interdisciplinary context we chose to rely on a common integration framework provided by a foundational ontology, that facilitates the consistent integration of the various modules extracted from several existing ontologies, i.e. FMA, PATO, MPATH, RadLex and ChEBI. Emphasis is put on methodology for achieving this extraction and integration. The most salient aspects of the ontology are presented, especially the organization in model layers, as well as its use to browse and query the model repository.

Connectivity within the primary motor cortex: a DTI tractography study.

PURPOSE: Because of the motor function of the precentral area, the connections of the primary motor cortex by white matter fiber bundles have been widely studied in diffusion tensor imaging (DTI). Nevertheless, the connections within the primary motor cortex have yet to be explored. We have studied the connectivity between the different regions of the precentral gyrus in a population of subjects. METHODS: Based on T1 magnetic resonance imaging (MRI) and on individual sulco-gyral anatomy, we defined a parcellation of the right and the left precentral gyri in 20 healthy subjects (10 right-handers; 10 left-handers). This parcellation gave us the opportunity to study MRI tracks reconstructed by tractography within the precentral gyrus and to compare these connections across subjects. We also performed a classical dissection of post-mortem brain tissue to isolate this pattern of connectivity. RESULTS: We showed MRI tracks connecting the different parts of the same precentral gyrus. This result was reproducible and was found in the left and right hemispheres of the 20 subjects. A quantitative description of the bilateral distribution of the MRI tracks was performed, based on statistical analysis and asymmetry indices, to compare asymmetry and handedness. CONCLUSIONS: To the best of our knowledge, this pattern of connectivity has never before been detailed in the literature. Its functional meaning remains to be determined, which requires further study.

A virtual imaging platform for multi-modality medical image simulation.

This paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011.

Characterization of short white matter fiber bundles in the central area from diffusion tensor MRI.

INTRODUCTION: Diffusion tensor imaging and tractography allow studying white matter fiber bundles in the human brain in vivo. Electrophysiological studies and postmortem dissections permit improving our knowledge about the short association fibers connecting the pre- and postcentral gyri. The aim of this study was first to extract and analyze the features of these short fiber bundles and secondly to analyze their asymmetry according to the subjects' handedness. METHODS: Ten right-handed and ten left-handed healthy subjects were included. White matter fiber bundles were extracted using a streamline tractography approach, with two seed regions of interest (ROI) taken from a parcellation of the pre- and postcentral gyri. This parcellation was achieved using T1 magnetic resonance images (MRI) and semi-automatically generated three ROIs within each gyrus. MRI tracks were reconstructed between all pairs of ROIs connecting the adjacent pre- and postcentral gyri. A quantitative analysis was performed on the number of tracks connecting each ROI pair. A statistical analysis studied the repartition of these MRI tracks in the right and left hemispheres and as a function of the subjects' handedness. RESULTS: The quantitative analysis showed an increased density of MRI tracks in the middle part of the central area in each hemisphere of the 20 subjects. The statistical analysis showed significantly more MRI tracks for the left hemisphere, when we consider the whole population, and this difference was presumably driven by the left-handers. CONCLUSION: These results raise questions about the functional role of these MRI tracks and their relation with laterality.

NeuroLOG: sharing neuroimaging data using an ontology-based federated approach.

This paper describes the design of the NeuroLOG middleware data management layer, which provides a platform to share heterogeneous and distributed neuroimaging data using a federated approach. The semantics of shared information is captured through a multi-layer application ontology and a derived Federated Schema used to align the heterogeneous database schemata from different legacy repositories. The system also provides a facility to translate the relational data into a semantic representation that can be queried using a semantic search engine thus enabling the exploitation of knowledge embedded in the ontology. This work shows the relevance of the distributed approach for neurosciences data management. Although more complex than a centralized approach, it is also more realistic when considering the federation of large data sets, and open strong perspectives to implement multi-centric neurosciences studies.