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DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in...

Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR.

PeerJ. 2016 May 24;4:e2057.

Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM(®)) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited in the QIN-HEADNECK collection of The Cancer Imaging Archive (TCIA). Supporting tools for data analysis and DICOM conversion were made available as free open-source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open-source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that the DICOM standard can be used to represent the types of data relevant in HNC QI biomarker development, and encode their complex relationships. The resulting annotated objects are amenable to data mining applications, and are interoperable with a variety of systems that support the DICOM standard.

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Read 15 Free eBooks on New Media Studies & the Digital Humanities

Read 15 Free eBooks on New Media Studies & the Digital Humanities | Library & information science |
Worth noting: digitalculturebooks is an imprint of the University of Michigan Press dedicated to publishing books on new media studies and digital humanities.

Via Giannis Lagamtzis
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Ontological Engineering

Ontological Engineering | Library & information science |
Barry Smith, “the ontology king”, has made freely available his Fall 2013 Ontological Engineering class. There is no better resource than here.

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Dmitry Alexeev's curator insight, November 19, 2013 11:04 AM

if one is to go deeper into ontology - there is a resource

we believe it will be the basis of data integration in biomed

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Guidelines for working with RDA and non-RDA records prior to implementation of RDA- Program for Cooperative Cataloging (Library of Congress)

Guidelines for working with RDA and non-RDA records prior to implementation of RDA- Program for Cooperative Cataloging (Library of Congress) | Library & information science |
>Guidelines for working with RDA and non-RDA records prior to implementation of RDA - Program for Cooperative Cataloging (Library of Congress)...


The following guidelines were recommended by the Task Group on Hybrid Bibliographic Records (Sept. 1, 2011). The recommendations were approved by the PCC Policy Committee. The documents include guidelines for working with RDA and non-RDA records for monographs, serials, and integrating resources prior to implementation of RDA.


The guidelines include PCC Task Group on Hybrid Integrating Resource Records (Word 97 KB) Final report, dated April 25, 2012: on recommendations and guidelines for creating a hybrid record from a pre-RDA record.


Check out the links here:

Via Fe Angela M. Verzosa
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Development of an open source software module for enhanced visualization during MR-guided interstitial gynecologic brachytherapy

Xiaojun Chen, Jan Egger


arXiv:1404.6116v1 [cs.SY]


In 2010, gynecologic malignancies were the 4th leading cause of death in U.S. women and for patients with extensive primary or recurrent disease, treatment with interstitial brachytherapy may be an option. However, brachytherapy requires precise insertion of hollow catheters with introducers into the tumor in order to eradicate the cancer. In this study, a software solution to assist interstitial gynecologic brachytherapy has been investigated and the software has been realized as an own module under (3D) Slicer, which is a free open source software platform for (translational) biomedical research. The developed research module allows on-time processing of intra-operative magnetic resonance imaging (iMRI) data over a direct DICOM connection to a MR scanner. Afterwards follows a multi-stage registration of CAD models of the medical brachytherapy devices (template, obturator) to the patient's MR images, enabling the virtual placement of interstitial needles to assist the physician during the intervention.

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Big Data Innovation, Issue 6

Big Data Innovation, Issue 6

Via Pantelis Chiotellis
Pantelis Chiotellis's curator insight, April 6, 2014 10:47 AM

Big Data Innovation Magazine, Issue 6

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Resource Description and Access (RDA)

Check out these websites to presentations in connection with the implementation of RDA:

*RDA Introduction - September 20, 2012

*RDA Discovery Day Presentation - March 4, 2011 (pps)

*RDA Preview - November 17, 2010 (ppt)


Other links to External Documentation:

Library of Congress "Information and Resources in Preparation for RDA":


LC/PCC Policy Statements:


Catalogers Learning Workshop:

OCLC policy on RDA (June 2011):


Program for Cooperative Cataloging

Frequently Asked Questions on PCC and RDA:


BIBCO Standard Record:


RDA Interim Policies and Best Practices:


Interim GUidelines for Working with RDA and non-RDA Records Prior to Implementation of RDA:


PCC Proposed Guidelines and Standards:




Changes from AACR2 to RDA: a comparison of examples, by Adam Schiff:


Complete examples for RDA Toolkit 2010:


LC examples comparing RDA with AACR2:


PCC RDA examples: training materials/SCT RDA Records TG/index.html


University of Chicago RDA examples:


Via Fe Angela M. Verzosa
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Career Paths for Geo Information Science Students

Career Paths for Geo Information Science Students | Library & information science |
The groundbreaking technology that is Geographic Information Science has become incredibly important to ways of life around the world.

Via Thomas Faltin
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