Author: McDonald CJ, Maglott D, Abhyankar S, Goodwin R, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G
US Realm, Chapter 5, Clinical Genomics Results Reporting. Published for May 2017 Ballot.
Abstract:No abstract available.
Author: Candemir S
Atlas-based lung boundary detection module (MATLAB Code)
We present to you software developed as part of the following article:
Candemir S, Jaeger S, Palaniappan K, Musco JP, Singh RK, Xue Z, Karargyris A, Antani S, Thoma G, McDonald CJ. Lung segmentation in chest radiographs using anatomical atlases with nonrigid registration. IEEE Trans Med Imaging. 2014 Feb; 33(2):577-90. doi: 10.1109/TMI.2013.2290491. PMID: 24239990
We request that you cite the paper if this code is used for publications or product.
The software contains the following assets:
- LungSegment_module.m: performs the lung segmentation on CXRs.
- Patient_Xrays: folder contain patient X-ray to be segmented. Please locate your test X-rays in this folder. The X-ray image can be in DICOM, TIFF, PNG, BMP, or JPEG file formats.
- Model_Xrays: folder contain example X-rays, their corresponding lung masks, vertical, and horizontal profiles. These X-rays and lung masks are used during registration process.
- Model_h.mat and Model_v.mat: precomputed profiles for model x-rays.
- TEST.m: to test the system, please run this function.
- subfunctions: CEB_polygionCurveEvolution.m, cebShape2Spline.m, f_removeBlackBorderds.m, f_RemoveSmallSegments.m, FindSimilarCXR.m, fitSpline.m, read_Xray.m, read_Xray.m, read_X_Mask.m, RegisterModel.m, SmoothBoundary.m (please refer code comments for these functions. )
The system is developed using MATLAB version 8.4 on 64-bit Intel architecture running Windows 7 operating system.
- Employed functions: mexDenseSIFT(m, mex), mesDiscreteFlow(m,mex), SIFTflowc2f.m functions are employed from the “SIFT Flow: Dense Correspondence across Scenes and Its applications”. Please use the http://people.csail.mit.edu/celiu/SIFTflow/ website to download the latest version of these functions. Do not forget citing the SIFTFlow paper.
How to run:
- Download and unpack the zip file containing the code here.
- Locate your CXRs in the Patient X-ray folder.
- Run the TEST.m function. The binary lung masks will be computed for each patient X-ray. The masks will be the same size as patient X-ray.
- Adjust parameters to obtain better results for your CXRs.
Contact: Stefan Jaeger
Author: Kilicoglu H
Bio-SCoRes is a general, modular framework for coreference resolution in biomedical text. It is underpinned by a smorgasbord architecture, and incorporates a variety of coreference types (anaphora, appositive, etc.), their textual expressions (definite noun phrases, possessive pronouns, etc.) and allows fine-grained specification of coreference resolution strategies. The tool includes the coreference resolution framework components and the linguistic components they rely on, as well as the coreference resolution pipelines that were used to evaluate the tool.
Download at https://github.com/kilicogluh/Bio-SCoRes
Author: Kayaalp M, Dodd Z, Browne AC, Sagan, P, McDonald CJ
Narrative clinical reports contain a rich set of clinical knowledge that could be invaluable for clinical research. However, they usually contain personal identifiers. The presence of personal identifiers in clinical reports renders the contents of those reports as protected health information, which is associated with use restrictions and risks to privacy. The Privacy Rule of Health Insurance Portability and Accountability Act (HIPAA) requires that clinical documents be stripped of personally identifying information before they can be released to researchers and others. Our solution, NLM-Scrubber, is a HIPAA compliant, clinical text de-identification tool designed and developed at the National Library of Medicine. It is freely available.
Author: Neve L, Long LR, Antani SK
Overview. The Boundary Marking Tool 2 (BMT2) was developed by the National Library of Medicine in collaboration with the National Cancer Institute. The BMT2 is software that allows the manual marking of boundaries on digitized images and the recording of diagnostic or interpretive data that applies to these individual boundaries, or to the image as a whole. It has been used in multiple studies by NCI of the correlation between visual observations of the cervix and biopsy-based diagnoses. It has been used in the NCI Biopsy Study, which aims to determine whether taking multiple biopsies at colposcopy will increase the detectability of high-grade cervix disease, and to develop a strategy for taking these biopsies. In 2014 van der Marel  recommended that taking multiple biopsies should become standard practice in colposcopy, following the study of data collected, using the BMT, for 610 patients in the Netherlands and Spain. In 2015 Wentzensen  reported on the results of analyzing data collected, using the BMT, from 690 patients at the University of Oklahoma, and made the same recommendation. In addition, in 2014, the BMT was used by the American Society for Colposcopy and Cervical Pathology (ASCCP) to mark up and review biopsy regions on cervix images for use in creating materials for proficiency exams in the field of colposcopy. The impact of the Boundary Marking Tool in biomedical research, as well as the impact of other software tools developed in the National Library of Medicine/National Cancer Institute collaboration, is summarized here.
We provide two alternative ways to use the BMT2.
First way (Download and Install Software): Download the Bundled BMT2 (NCI Biopsy Study BMT2); this is a Microsoft Windows setup file which installs the BMT2 and all required software on your computer (namely MySQL, Tomcat and Java if necessary), and asks you to agree to a license regarding its proper use and redistribution. This is the way that the National Cancer Institute is currently using the BMT2 to mark images acquired from digital cameras, and to store the marked images locally, without requiring an Internet connection. This approach offers a bundled installation which gets you up and running quickly without requiring anything additional.Download the Bundled BMT2 (NCI Biopsy Study BMT2) setup file here (https://ceb.nlm.nih.gov/imsbmt/bmt_setup.exe). Then follow these installation instructions.
Second way (Web Interface): Run the BMT2 directly from our NLM Communications Engineering Branch website with a user account that we can provide. This approach allows you to run the BMT2 on any type of computer (Mac, Linux, etc.) with Oracle's Java 1.5 or greater installed. Request a BMT2 account here (https://www.nlm.nih.gov/research/researchstaff/AntaniSameer.html). Then launch the BMT2.
Van der Marel J, Schiffman M, Wentzensen N, et al. The increased detection of cervical intraepithelial neoplasia when using a second biopsy at colposcopy. Gynecologic Oncology, Nov. 2014, 135(2):201-7.
Wentzensen N, Zuna RE, Schiffman M, et al. Multiple biopsies and detection of cervical cancer precursors at colposcopy. Journal of Clinical Oncology, Jan. 2015, 33(1):83-9.
Author: Lowekamp B, Chen D, Santoroski J, Yaniv Z, Yoo TS
SimpleITK is a layer built on top of ITK to facilitate ITK's use in rapid prototyping, education, and interpreted languages. Its main characteristics are:
- C++ library
- Simple easy-to-use procedural interface without templates
- Distributed under an open source Apache 2.0 License
- Available for the following programing languages: Python, R, Java, C#, C++, Lua, Ruby, and TCL
More information is at http://www.simpleitk.org/
Author: Thoma GR, Ford G, Demner-Fushman D, Antani SK, Chung M
Important results of scientific studies in life sciences are traditionally communicated through journal publications. Internet provides a venue for multimedia journal articles, mostly implemented as textual documents containing hyperlinks to video clips, 3D images, etc.
We propose tools for authoring and viewing the next generation of multimedia documents: Interactive Publications (IP). An IP is a self-contained multimedia document, which, in addition to presenting a study and its results, provides access to the underlying data and a possibly to manipulate the data, thus becoming a research tool.
The authoring tool (Forge) and the viewer (Panorama) are being implemented in Java using the Eclipse Rich Client Platform, work with PDF files, and provide an opportunity to view, link, and manipulate data, as well as to customize the tool through a set of graphic controls and transparently to the user. The tool is configured internally through XML files that define the media location and the views to be presented. Panorama currently supports: charts, graphs, and built-in basic statistics as overlays on charts; video with chapters; multi-slice clinical images in the DICOM format; 3D rendering; and an integrated browser.
Author: Lowekamp B, Yoo TS
The Insight Toolkit (ITK) is an open-source software toolkit for performing registration (alignment) and segmentation (partitioning) of biomedical image data. It was developed under contract to NLM by three commercial partners (Kitware, GE Corporate R&D, and Insightful) and three academic partners (UNC Chapel Hill, University of Utah, and University of Pennsylvania). ITK supports NLM's Visible Human Project®.
- Download ITK software: http://www.itk.org/ITK/resources/software.html
- Download SimpleITK software: http://www.kitware.com/news/home/browse/ITK?2013_02_18&SimpleITK+0.6.1+is+Now+Available+for+Download%21
- Copyright and license: http://www.itk.org/ITK/project/license.html
- Learn more: http://itk.org