The document discusses a crowdsourcing experiment conducted at RSNA 2018 to collect cancer image annotations from over 250 participants. Preliminary results found promising agreement between crowd annotations and expert ground truths. Feedback from participants suggested improvements to the annotation interface such as tutorials, measurement tools, and metrics display. Overall the experiment demonstrated the potential for crowdsourcing to efficiently generate large annotated medical image datasets.
Public Databases for Radiomics Research: Current Status and Future DirectionsCancerImagingInforma
This document discusses radiomics research and public databases. It describes what radiomics is and why data sharing is important. Several public databases are mentioned, with an in-depth look at The Cancer Imaging Archive (TCIA). TCIA hosts radiology data like CT, MR, PET images along with associated data. It provides services to upload and access data and enables data citation. Future directions discussed include standardization initiatives and using cloud computing.
Advancing Convergence and Innovation in Cancer Research: Seminar at Universit...Jerry Lee
Since 2003, the National Cancer Institute’s Center for Strategic Scientific Initiatives (CSSI) has worked to develop the resources and infrastructures investigators need to surmount roadblocks in cancer research. CSSI manages programs that promote technology development and cross-disciplinary collaboration and provide support for investigators in nascent and challenging research fields. This support includes funding opportunities, shared reagent and database resources, and assistance in the development of standards and protocols. CSSI also provides a network of partners in industry and government that can help NCI-funded researchers advance their technologies toward commercialization and translation. This presentation will highlight technologies including single-cell isolation and analysis techniques that have been supported through various CSSI mechanisms from proof-of-concept to translation into the clinic.
Advancing Convergence and Innovation in Cancer ResearchJerry Lee
Describes NCI's Center for Strategic Scientific Initiatives activities (2005 - 2017) as well as data and technology activities of the 2016 White House Cancer Moonshot Task Force (2016 - 2017).
The Cancer Imaging Archive (TCIA) is a large online archive of medical images and associated clinical data from cancer patients. It contains a variety of imaging modalities like CT, MRI, and PET scans covering many cancer types. The archive aims to support precision medicine by linking imaging data to molecular and genomic data from sources like The Cancer Genome Atlas. It provides a growing collection of over 40,000 subjects and 70 datasets that are frequently used in research publications and challenge competitions. The TCIA helps relieve researchers of data sharing burdens and provides hosting, de-identification, and support services to submitters and users of the archive.
Quantitative methods of data collection and its importance
The document discusses quantitative methods of data collection, which use numerical and statistical processes to answer specific questions. It describes several types of quantitative data collection, including census, sample surveys, experiments, and observational studies. The document also outlines some key methods used in cancer diagnosis, such as imaging procedures, biopsies, and the significance of environmental and genetic factors in cancer causation. Treatment methods for cancer discussed include surgery, radiation therapy, chemotherapy, immunotherapy, targeted therapy, and hormone therapy.
BDW16 London - Mishal Patel, NHS - Modernising Routine Breast Cancer Using Bi...Big Data Week
Radiological imaging is fundamental within the healthcare industry and has become routinely adopted for diagnosis, disease monitoring and treatment planning. With the advent of digital imaging modalities and the rapid growth in both diagnostic and therapeutic imaging, the ability to able to harness this large influx of data is of paramount. Traditionally, the systematic collection of medical images for research from heterogeneous sites has not been commonplace within the NHS and is fraught with challenges including; data acquisition, storage, secure transfer and correct anonymisation. Here we describe the development and implementation of a national centralised oncology image database and discuss the central issues associated with large-scale image acquisition from heterogeneous sites.
The ability to collect fully annotated sets of images for research opens to door to a multitude of potential research opportunities that utilise the legacy images, such as quantitative image informatics. Medical imaging provides the ability to detect and localise many changes that are important to determine whether a disease is present or a therapy is effective by depicting alterations in the anatomic, physiologic, biochemical or molecular process. Calculating quantitative imaging features from acquired images and using these to build computational models to investigate detection, prognosis, and classification.
The Value of Multimedia-Enhanced Radiology ReportingCarestream
Statistics from the American College of Radiology study,“Traditional Text-Only Versus Multimedia-Enhanced Radiology Reporting: Referring Physicians’ Perceptions of Value," explains how valuable referring physicians believe multimedia radiology report to be.
Scott Edmunds: GigaScience - a journal or a database? Lessons learned from th...GigaScience, BGI Hong Kong
Scott Edmunds talk at the HUPO congress in Geneva, September 6th 2011 on GigaScience - a journal or a database? Lessons learned from the Genomics Tsunami.
Public Databases for Radiomics Research: Current Status and Future DirectionsCancerImagingInforma
This document discusses radiomics research and public databases. It describes what radiomics is and why data sharing is important. Several public databases are mentioned, with an in-depth look at The Cancer Imaging Archive (TCIA). TCIA hosts radiology data like CT, MR, PET images along with associated data. It provides services to upload and access data and enables data citation. Future directions discussed include standardization initiatives and using cloud computing.
Advancing Convergence and Innovation in Cancer Research: Seminar at Universit...Jerry Lee
Since 2003, the National Cancer Institute’s Center for Strategic Scientific Initiatives (CSSI) has worked to develop the resources and infrastructures investigators need to surmount roadblocks in cancer research. CSSI manages programs that promote technology development and cross-disciplinary collaboration and provide support for investigators in nascent and challenging research fields. This support includes funding opportunities, shared reagent and database resources, and assistance in the development of standards and protocols. CSSI also provides a network of partners in industry and government that can help NCI-funded researchers advance their technologies toward commercialization and translation. This presentation will highlight technologies including single-cell isolation and analysis techniques that have been supported through various CSSI mechanisms from proof-of-concept to translation into the clinic.
Advancing Convergence and Innovation in Cancer ResearchJerry Lee
Describes NCI's Center for Strategic Scientific Initiatives activities (2005 - 2017) as well as data and technology activities of the 2016 White House Cancer Moonshot Task Force (2016 - 2017).
The Cancer Imaging Archive (TCIA) is a large online archive of medical images and associated clinical data from cancer patients. It contains a variety of imaging modalities like CT, MRI, and PET scans covering many cancer types. The archive aims to support precision medicine by linking imaging data to molecular and genomic data from sources like The Cancer Genome Atlas. It provides a growing collection of over 40,000 subjects and 70 datasets that are frequently used in research publications and challenge competitions. The TCIA helps relieve researchers of data sharing burdens and provides hosting, de-identification, and support services to submitters and users of the archive.
Quantitative methods of data collection and its importance
The document discusses quantitative methods of data collection, which use numerical and statistical processes to answer specific questions. It describes several types of quantitative data collection, including census, sample surveys, experiments, and observational studies. The document also outlines some key methods used in cancer diagnosis, such as imaging procedures, biopsies, and the significance of environmental and genetic factors in cancer causation. Treatment methods for cancer discussed include surgery, radiation therapy, chemotherapy, immunotherapy, targeted therapy, and hormone therapy.
BDW16 London - Mishal Patel, NHS - Modernising Routine Breast Cancer Using Bi...Big Data Week
Radiological imaging is fundamental within the healthcare industry and has become routinely adopted for diagnosis, disease monitoring and treatment planning. With the advent of digital imaging modalities and the rapid growth in both diagnostic and therapeutic imaging, the ability to able to harness this large influx of data is of paramount. Traditionally, the systematic collection of medical images for research from heterogeneous sites has not been commonplace within the NHS and is fraught with challenges including; data acquisition, storage, secure transfer and correct anonymisation. Here we describe the development and implementation of a national centralised oncology image database and discuss the central issues associated with large-scale image acquisition from heterogeneous sites.
The ability to collect fully annotated sets of images for research opens to door to a multitude of potential research opportunities that utilise the legacy images, such as quantitative image informatics. Medical imaging provides the ability to detect and localise many changes that are important to determine whether a disease is present or a therapy is effective by depicting alterations in the anatomic, physiologic, biochemical or molecular process. Calculating quantitative imaging features from acquired images and using these to build computational models to investigate detection, prognosis, and classification.
The Value of Multimedia-Enhanced Radiology ReportingCarestream
Statistics from the American College of Radiology study,“Traditional Text-Only Versus Multimedia-Enhanced Radiology Reporting: Referring Physicians’ Perceptions of Value," explains how valuable referring physicians believe multimedia radiology report to be.
Scott Edmunds: GigaScience - a journal or a database? Lessons learned from th...GigaScience, BGI Hong Kong
Scott Edmunds talk at the HUPO congress in Geneva, September 6th 2011 on GigaScience - a journal or a database? Lessons learned from the Genomics Tsunami.
WEBINAR: The Yosemite Project PART 6 -- Data-Driven Biomedical Research with ...DATAVERSITY
In this presentation, our speaker, Dr. Michel Dumontier, will explore the use of Semantic Web technologies to reduce the overwhelming burden of integrating clinical data with public biomedical data, and enabling a new generation of translational research and their clinical application.
Theralase Technologies Inc. (TSX-V: TLT) announced today the successful results of preclinical studies (in-vitro and in-vivo) demonstrating significant destruction of various brain and colon cancer cell lines. The new proprietary Theralase treatment sharply delayed the tumour progression, when attacked by the Theralase patented light activated Photo Dynamic Compounds (PDCs), signifying a new and broadly promising approach to cancer treatment. When treated with the Theralase PDCs, cancerous mice survived cancer-free for more than 100 days post-treatment, a highly significant milestone.
Universal access to virtual colonoscopy may be on the horizonYael Waknine
Virtual colonoscopy (CT colonography) has been endorsed by several medical organizations since 2008 as a screening method for colorectal cancer. However, it is not covered by Medicare for reimbursement due to political opposition from organizations supporting traditional colonoscopy and concerns about risks. Radiologists argue that many of the original concerns about virtual colonoscopy have been addressed by peer-reviewed research showing it is a safe and cost-effective screening option. They call for public advocacy to change the test's rating by the US Preventive Services Task Force in order to gain Medicare coverage, which would significantly boost low colorectal cancer screening rates in the US.
NCI Cancer Imaging Program - Cancer Research Data EcosystemWarren Kibbe
Given to the NCI Cancer Imaging Program monthly telecon on January 9th, 2017. NCI Genomic Data Commons, Beau Biden Cancer Moonshot Blue Ribbon Panel, Cancer Research Data Ecosystem and the role of imaging in precision medicine
Next Generation Companion Diagnostics; Adoption, Drivers, and Moderators of N...Andrew Aijian
Analysis and synthesis of a pulse survey conducted across >140 oncologists, pathologists, and lab directors regarding current adoption and trends associated with emerging oncology biomarkers and companion diagnostics (CDx), with an emphasis on next-generation sequencing (NGS)-based CDx.
1) 23andMe was founded 2.5 years ago to provide consumers access to their genetic data and participate in genetic research.
2) It has grown to analyze DNA for over 35,000 individuals, making it one of the largest genetic databases.
3) Through participant-driven studies, 23andMe has identified novel genetic associations for many common traits and diseases, including identifying several genes associated with Parkinson's disease through its Parkinson's Project.
GenomeTrakr: Perspectives on linking internationally - Canada and IRIDA.cafionabrinkman
Talk at GenomeTrakr network meeting Sept 23 2015 in Washington DC. On Canada's open source Integrated Rapid Infectious Disease Analysis (IRIDA) bioinformatics platform - aiding genomic epidemiology analysis for public health agencies with planned open data release and linkage to GenomeTrakr. Discussed perspectives, challenges, solutions for getting more GenomeTrakr participation internationally.
Towards Digitally Enabled Genomic Medicine: the Patient of The FutureLarry Smarr
12.02.22
Invited Speaker
Hacking Life
TTI/Vanguard Conference
Title: Towards Digitally Enabled Genomic Medicine: the Patient of The Future
San Jose, CA
Is the increasing availability of automated image analysis a possibility to strengthen the application of diffusion-MRI as a biometric parameter, and to enhance the future of image biobanks? Or is this evolution threatening the position of radiologists as medical doctors. Is a redefinition of radiologist as computer technicians inevitable?
Published on Feb 07, 2016 by PMR
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus. Includes clips of the software in action
Professor Carole Goble, University of Manchester, talks at the RIN "Research data: policies & behaviour" event as part of a series on Research Information in Transition.
Using Public Access Clinical Databases to Interpret NGS VariantsGolden Helix Inc
In this webcast on February 19th, Gabe Rudy, Vice President of Product Development, will showcase publicly available databases and resources available for interpreting rare and novel mutations in the context of his own personal exome obtained through a limited 23andMe pilot in 2012.
The last couple years have seen many changes in well-established resources such as OMIM and dbSNP, while motivating new efforts such as ClinVar and PhenoDB to bring NGS interpretation to clinical grade through a global data sharing effort.
In this webcast, Gabe will cover:
The changing landscape of public annotations: Then, Now, and Soon.
Will the new human reference (GRCh38) released in December be a game changer?
Specific examples of improvements in annotation and algorithms that result in more accurate analysis of his own exome.
The utility and progress of NGS to different clinical applications in terms of public resources: carrier screening, hereditary cancer risk, pharmacogenomics, oncology care, and genetic disorder diagnosis.
Sharing of new clinical data: How both variation and phenotype level data is currently being shared and what will be the way forward to match rare and undiagnosed cases at a global scale.
Computational Pathology Workshop July 8 2014Joel Saltz
This document discusses computational pathology research. It describes using computational methods like high dimensional fused informatics, image analysis, and machine learning to analyze pathology images and integrate them with genomic and clinical data. The goals are to characterize tumors at multiple scales, predict treatment outcomes, and identify tumor subtypes. Challenges include managing the large amounts of image and multi-dimensional data generated. The document outlines several of Joel Saltz's pathology research projects and computational pathology initiatives like challenges that integrate radiology, pathology, and genomic data to predict patient outcomes.
1) Quantitative medicine uses large amounts of medical data and advanced analytics to determine the most effective treatment for individual patients based on their specific clinical profile and biomarkers. This approach can help reduce healthcare costs and improve outcomes compared to the traditional one-size-fits-all model.
2) However, realizing the promise of quantitative personalized medicine is challenging due to the huge quantities of diverse medical data located in dispersed systems, lack of computing capabilities, and barriers to data sharing.
3) Grid and service-oriented computing approaches are helping to address these challenges by enabling federated querying, analysis, and sharing of medical data and services across organizations through virtual integration rather than true consolidation.
tranSMART Community Meeting 5-7 Nov 13 - Session 3: The TraIT user stories fo...David Peyruc
This document provides an overview of the TraIT project and existing demonstrators using tranSMART. It discusses the TraIT roadmap and user stories being implemented at the Netherlands Cancer Institute. Key points include:
- TraIT aims to support translational research through integrated data and tools across clinical, imaging, biobanking and experimental domains.
- Existing demonstrators using tranSMART include DeCoDe (colorectal cancer) and PCMM (prostate cancer).
- The roadmap involves enhancing tranSMART functionality based on user needs and integrating additional data sources.
- At NKI, tranSMART will provide an integrated research data warehouse with clinical and research data from various sources and departments.
tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the c...David Peyruc
tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the cell phenotypes involved in metastasis
Characterization of the cell phenotypes involved in metastasis: Using tranSMART to enable high-throughput heterogeneous data integration and analysis
Brian Athey, University of Michigan
American Association for Cancer Research Annual Meeting 2022
Analysis of images of routinely acquired tissue specimens promise to provide biomarkers that can be used to predict disease outcome and steer treatment, improve diagnostic reproducibility, and reveal new insights to further advance current human understanding of disease. The advent of AI and ubiquitous high-end computing are making it possible to carry out accurate whole slide image morphological and molecular tissue analyses at cellular and subcellular resolutions. AI methods are can enable exploration and discovery of novel diagnostic biomarkers grounded in prognostically predictive spatial and molecular patterns as well as quantitative assessments of predictive value and reproducibility of traditional morphological patterns employed in anatomic pathology. AI methods may be adapted to help steer treatment through integrative analysis of clinical information along with Pathology, Radiology and molecular data.
WEBINAR: The Yosemite Project PART 6 -- Data-Driven Biomedical Research with ...DATAVERSITY
In this presentation, our speaker, Dr. Michel Dumontier, will explore the use of Semantic Web technologies to reduce the overwhelming burden of integrating clinical data with public biomedical data, and enabling a new generation of translational research and their clinical application.
Theralase Technologies Inc. (TSX-V: TLT) announced today the successful results of preclinical studies (in-vitro and in-vivo) demonstrating significant destruction of various brain and colon cancer cell lines. The new proprietary Theralase treatment sharply delayed the tumour progression, when attacked by the Theralase patented light activated Photo Dynamic Compounds (PDCs), signifying a new and broadly promising approach to cancer treatment. When treated with the Theralase PDCs, cancerous mice survived cancer-free for more than 100 days post-treatment, a highly significant milestone.
Universal access to virtual colonoscopy may be on the horizonYael Waknine
Virtual colonoscopy (CT colonography) has been endorsed by several medical organizations since 2008 as a screening method for colorectal cancer. However, it is not covered by Medicare for reimbursement due to political opposition from organizations supporting traditional colonoscopy and concerns about risks. Radiologists argue that many of the original concerns about virtual colonoscopy have been addressed by peer-reviewed research showing it is a safe and cost-effective screening option. They call for public advocacy to change the test's rating by the US Preventive Services Task Force in order to gain Medicare coverage, which would significantly boost low colorectal cancer screening rates in the US.
NCI Cancer Imaging Program - Cancer Research Data EcosystemWarren Kibbe
Given to the NCI Cancer Imaging Program monthly telecon on January 9th, 2017. NCI Genomic Data Commons, Beau Biden Cancer Moonshot Blue Ribbon Panel, Cancer Research Data Ecosystem and the role of imaging in precision medicine
Next Generation Companion Diagnostics; Adoption, Drivers, and Moderators of N...Andrew Aijian
Analysis and synthesis of a pulse survey conducted across >140 oncologists, pathologists, and lab directors regarding current adoption and trends associated with emerging oncology biomarkers and companion diagnostics (CDx), with an emphasis on next-generation sequencing (NGS)-based CDx.
1) 23andMe was founded 2.5 years ago to provide consumers access to their genetic data and participate in genetic research.
2) It has grown to analyze DNA for over 35,000 individuals, making it one of the largest genetic databases.
3) Through participant-driven studies, 23andMe has identified novel genetic associations for many common traits and diseases, including identifying several genes associated with Parkinson's disease through its Parkinson's Project.
GenomeTrakr: Perspectives on linking internationally - Canada and IRIDA.cafionabrinkman
Talk at GenomeTrakr network meeting Sept 23 2015 in Washington DC. On Canada's open source Integrated Rapid Infectious Disease Analysis (IRIDA) bioinformatics platform - aiding genomic epidemiology analysis for public health agencies with planned open data release and linkage to GenomeTrakr. Discussed perspectives, challenges, solutions for getting more GenomeTrakr participation internationally.
Towards Digitally Enabled Genomic Medicine: the Patient of The FutureLarry Smarr
12.02.22
Invited Speaker
Hacking Life
TTI/Vanguard Conference
Title: Towards Digitally Enabled Genomic Medicine: the Patient of The Future
San Jose, CA
Is the increasing availability of automated image analysis a possibility to strengthen the application of diffusion-MRI as a biometric parameter, and to enhance the future of image biobanks? Or is this evolution threatening the position of radiologists as medical doctors. Is a redefinition of radiologist as computer technicians inevitable?
Published on Feb 07, 2016 by PMR
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus. Includes clips of the software in action
Professor Carole Goble, University of Manchester, talks at the RIN "Research data: policies & behaviour" event as part of a series on Research Information in Transition.
Using Public Access Clinical Databases to Interpret NGS VariantsGolden Helix Inc
In this webcast on February 19th, Gabe Rudy, Vice President of Product Development, will showcase publicly available databases and resources available for interpreting rare and novel mutations in the context of his own personal exome obtained through a limited 23andMe pilot in 2012.
The last couple years have seen many changes in well-established resources such as OMIM and dbSNP, while motivating new efforts such as ClinVar and PhenoDB to bring NGS interpretation to clinical grade through a global data sharing effort.
In this webcast, Gabe will cover:
The changing landscape of public annotations: Then, Now, and Soon.
Will the new human reference (GRCh38) released in December be a game changer?
Specific examples of improvements in annotation and algorithms that result in more accurate analysis of his own exome.
The utility and progress of NGS to different clinical applications in terms of public resources: carrier screening, hereditary cancer risk, pharmacogenomics, oncology care, and genetic disorder diagnosis.
Sharing of new clinical data: How both variation and phenotype level data is currently being shared and what will be the way forward to match rare and undiagnosed cases at a global scale.
Computational Pathology Workshop July 8 2014Joel Saltz
This document discusses computational pathology research. It describes using computational methods like high dimensional fused informatics, image analysis, and machine learning to analyze pathology images and integrate them with genomic and clinical data. The goals are to characterize tumors at multiple scales, predict treatment outcomes, and identify tumor subtypes. Challenges include managing the large amounts of image and multi-dimensional data generated. The document outlines several of Joel Saltz's pathology research projects and computational pathology initiatives like challenges that integrate radiology, pathology, and genomic data to predict patient outcomes.
1) Quantitative medicine uses large amounts of medical data and advanced analytics to determine the most effective treatment for individual patients based on their specific clinical profile and biomarkers. This approach can help reduce healthcare costs and improve outcomes compared to the traditional one-size-fits-all model.
2) However, realizing the promise of quantitative personalized medicine is challenging due to the huge quantities of diverse medical data located in dispersed systems, lack of computing capabilities, and barriers to data sharing.
3) Grid and service-oriented computing approaches are helping to address these challenges by enabling federated querying, analysis, and sharing of medical data and services across organizations through virtual integration rather than true consolidation.
tranSMART Community Meeting 5-7 Nov 13 - Session 3: The TraIT user stories fo...David Peyruc
This document provides an overview of the TraIT project and existing demonstrators using tranSMART. It discusses the TraIT roadmap and user stories being implemented at the Netherlands Cancer Institute. Key points include:
- TraIT aims to support translational research through integrated data and tools across clinical, imaging, biobanking and experimental domains.
- Existing demonstrators using tranSMART include DeCoDe (colorectal cancer) and PCMM (prostate cancer).
- The roadmap involves enhancing tranSMART functionality based on user needs and integrating additional data sources.
- At NKI, tranSMART will provide an integrated research data warehouse with clinical and research data from various sources and departments.
tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the c...David Peyruc
tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the cell phenotypes involved in metastasis
Characterization of the cell phenotypes involved in metastasis: Using tranSMART to enable high-throughput heterogeneous data integration and analysis
Brian Athey, University of Michigan
American Association for Cancer Research Annual Meeting 2022
Analysis of images of routinely acquired tissue specimens promise to provide biomarkers that can be used to predict disease outcome and steer treatment, improve diagnostic reproducibility, and reveal new insights to further advance current human understanding of disease. The advent of AI and ubiquitous high-end computing are making it possible to carry out accurate whole slide image morphological and molecular tissue analyses at cellular and subcellular resolutions. AI methods are can enable exploration and discovery of novel diagnostic biomarkers grounded in prognostically predictive spatial and molecular patterns as well as quantitative assessments of predictive value and reproducibility of traditional morphological patterns employed in anatomic pathology. AI methods may be adapted to help steer treatment through integrative analysis of clinical information along with Pathology, Radiology and molecular data.
Next generation electronic medical records and search a test implementation i...lucenerevolution
Presented by David Piraino, Chief Imaging Information Officer, Imaging Institute Cleveland Clinic, Cleveland Clinic
& Daniel Palmer, Chief Imaging Information Officer, Imaging Institute Cleveland Clinic, Cleveland Clinic
Most patient specifc medical information is document oriented with varying amounts of associated meta-data. Most of pateint medical information is textual and semi-structured. Electronic Medical Record Systems (EMR) are not optimized to present the textual information to users in the most understandable ways. Present EMRs show information to the user in a reverse time oriented patient specific manner only. This talk discribes the construction and use of Solr search technologies to provide relevant historical information at the point of care while intepreting radiology images.
Radiology reports over a 4 year period were extracted from our Radiology Information System (RIS) and passed through a text processing engine to extract the results, impression, exam description, location, history, and date. Fifteen cases reported during clinical practice were used as test cases to determine if ""similar"" historical cases were found . The results were evaluated by the number of searches that returned any result in less than 3 seconds and the number of cases that illustrated the questioned diagnosis in the top 10 results returned as determined by a bone and joint radiologist. Also methods to better optimize the search results were reviewed.
An average of 7.8 out of the 10 highest rated reports showed a similar case highly related to the present case. The best search showed 10 out of 10 cases that were good examples and the lowest match search showed 2 out of 10 cases that were good examples.The talk will highlight this specific use case and the issues and advances of using Solr search technology in medicine with focus on point of care applications.
Advancing Innovation and Convergence in Cancer Research: US Federal Cancer Mo...Jerry Lee
Special Seminar at the 8th Taiwan Biosignatures Workshop to share overall work of NCI's Center for Strategic Scientific Initiatives since 2003 as well as CSSI's influence on select projects initiated by the 2016 WH Cancer Moonshot Task Force that include Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) network, International Cancer Proteogenome Consortium, and the Blood Profiling Atlas in Cancer (BloodPAC) commons.
University of Toronto - Radiomics for Oncology - 2017Andre Dekker
This document contains the slides from a lecture on radiomics for oncology given by Andre Dekker. The lecture covers the rationale for radiomics, which is to use quantitative features extracted from medical images to help predict outcomes like tumor behavior, survival, and response to treatment using machine learning. The major workflow steps of radiomics are discussed, from image acquisition and feature extraction to modeling and validation. Key challenges like robust segmentation and feature reproducibility are also addressed. New directions for radiomics research include applications in preclinical studies, other modalities like PET and MRI, and linking radiomic features to genomic data. Overall, radiomics holds promise to help personalized medicine but large amounts of standardized data are still needed for proper validation of models.
A series project visualization too for review of DICOM images for protected health information
presented by William Bennett during the January 7, 2019 NCI Imaging Community call
Generation and Use of Quantitative Pathology PhenotypeJoel Saltz
Motivation, tools and methods analysis of digital pathology imagery, integration with "omics" and Radiology, use in Precision Medicine. Presentation at the Early Detection Research Network meeting, April 2015, Atlanta GA
I gave this talk in the "Presidential Symposium" at the annual meeting of the American Association of Physicists in Medicine, in Annaheim, California. The President of AAPM, Dr. Maryellen Giger, wanted some people to give some visionary talks. She invited (I kid you not) Foster, Gates, and Obama. Fortunately Bill and Barack had other commitments, so I did not need to share the time with them.
This document discusses Moffitt Cancer Center's Total Cancer Care program which aims to transform cancer care through a personalized approach. It involves collecting extensive clinical, molecular, and biospecimen data from patients over their lifetime to power research. The goals are to improve outcomes through early detection, personalized treatment, and clinical trials matching. Moffitt has established an extensive biorepository and informatics platform to integrate data from over 78,000 consented patients to enable precision oncology research.
- The document discusses the Total Cancer Care (TCC) approach at Moffitt Cancer Center, which aims to provide personalized cancer care through comprehensive data collection and analysis.
- TCC collects extensive clinical, genomic, treatment and outcomes data from over 78,000 consented patients to power research studies and clinical trials matching. Molecular profiling has been conducted on over 14,000 tumor samples.
- The TCC data is housed in a large integrated database and used by researchers for studies in areas like radiochemotherapy response, exome sequencing, immunology biomarkers, and cancer epidemiology.
- The database also helps clinicians identify eligible patients for clinical trials and develop evidence-based treatment pathways. The goal is to transform cancer
Radiomics Data Management, Computation, and Analysis for QIN F2F 2016Ashish Sharma
Large Scale Data Management Computation and Analysis for Quantitative Imaging Research
Talk at the 2016 QIN Annual Meeting — covers resources developed for the Quantitative Imaging Network. Includes TCIA data curation, APIs, supported data types, as well as co-located computing and systematic phenotyping of imaging biomarkers
The Clinical and Molecular Epidemiology Shared Resource (CMESR) provides services including the collection, processing, and storage of biological samples and clinical data from various cancer patient populations. It assists with IRB protocols, questionnaire data entry and analysis, and sample and data requests for cancer research. The CMESR is located at the Lombardi Cancer Center and houses samples and data on prostate, head and neck, colon, lung, and breast cancers.
Ontology-Driven Clinical Intelligence: A Path from the Biobank to Cross-Disea...Remedy Informatics
The discovery of clinical insights through effective management and reuse of data requires several conditions to be optimized: Data need to be digital, data need to be structured, and data need to be standardized in terms of metadata and ontology. This presentation describes a bioinformatics system that combines a next-generation biobank management model mapped to applicable international standards and guidelines with a master ontology that controls all input and output and is able to add unique properties to meet the specialized needs of clinicians for cross-disease research.
Workshop finding and accessing data - fiona - lunteren april 18 2016Fiona Nielsen
Workshop presentation on finding and accessing human genomics data for research.
Including statistics of publicly available data sources and tips on how to save time in your workflow of data access.
Presented at BioSB2016, pre-conference PhD retreat for young researchers in bioinformatics and systems biology at Congrescentrum De Werelt in Lunteren. #BioSB2016 #BioSB16
Link to event:
http://www.youngcb.nl/events/biosb-phd-retreat-2016/
Read more about my work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
Similar to Crowds Cure Canver: Annotating Data from The Cancer Imaging Archive (20)
Here is the updated list of Top Best Ayurvedic medicine for Gas and Indigestion and those are Gas-O-Go Syp for Dyspepsia | Lavizyme Syrup for Acidity | Yumzyme Hepatoprotective Capsules etc
Muktapishti is a traditional Ayurvedic preparation made from Shoditha Mukta (Purified Pearl), is believed to help regulate thyroid function and reduce symptoms of hyperthyroidism due to its cooling and balancing properties. Clinical evidence on its efficacy remains limited, necessitating further research to validate its therapeutic benefits.
8 Surprising Reasons To Meditate 40 Minutes A Day That Can Change Your Life.pptxHolistified Wellness
We’re talking about Vedic Meditation, a form of meditation that has been around for at least 5,000 years. Back then, the people who lived in the Indus Valley, now known as India and Pakistan, practised meditation as a fundamental part of daily life. This knowledge that has given us yoga and Ayurveda, was known as Veda, hence the name Vedic. And though there are some written records, the practice has been passed down verbally from generation to generation.
ABDOMINAL TRAUMA in pediatrics part one.drhasanrajab
Abdominal trauma in pediatrics refers to injuries or damage to the abdominal organs in children. It can occur due to various causes such as falls, motor vehicle accidents, sports-related injuries, and physical abuse. Children are more vulnerable to abdominal trauma due to their unique anatomical and physiological characteristics. Signs and symptoms include abdominal pain, tenderness, distension, vomiting, and signs of shock. Diagnosis involves physical examination, imaging studies, and laboratory tests. Management depends on the severity and may involve conservative treatment or surgical intervention. Prevention is crucial in reducing the incidence of abdominal trauma in children.
Adhd Medication Shortage Uk - trinexpharmacy.comreignlana06
The UK is currently facing a Adhd Medication Shortage Uk, which has left many patients and their families grappling with uncertainty and frustration. ADHD, or Attention Deficit Hyperactivity Disorder, is a chronic condition that requires consistent medication to manage effectively. This shortage has highlighted the critical role these medications play in the daily lives of those affected by ADHD. Contact : +1 (747) 209 – 3649 E-mail : sales@trinexpharmacy.com
Osteoporosis - Definition , Evaluation and Management .pdfJim Jacob Roy
Osteoporosis is an increasing cause of morbidity among the elderly.
In this document , a brief outline of osteoporosis is given , including the risk factors of osteoporosis fractures , the indications for testing bone mineral density and the management of osteoporosis
NVBDCP.pptx Nation vector borne disease control programSapna Thakur
NVBDCP was launched in 2003-2004 . Vector-Borne Disease: Disease that results from an infection transmitted to humans and other animals by blood-feeding arthropods, such as mosquitoes, ticks, and fleas. Examples of vector-borne diseases include Dengue fever, West Nile Virus, Lyme disease, and malaria.
Basavarajeeyam is an important text for ayurvedic physician belonging to andhra pradehs. It is a popular compendium in various parts of our country as well as in andhra pradesh. The content of the text was presented in sanskrit and telugu language (Bilingual). One of the most famous book in ayurvedic pharmaceutics and therapeutics. This book contains 25 chapters called as prakaranas. Many rasaoushadis were explained, pioneer of dhatu druti, nadi pareeksha, mutra pareeksha etc. Belongs to the period of 15-16 century. New diseases like upadamsha, phiranga rogas are explained.
Rasamanikya is a excellent preparation in the field of Rasashastra, it is used in various Kushtha Roga, Shwasa, Vicharchika, Bhagandara, Vatarakta, and Phiranga Roga. In this article Preparation& Comparative analytical profile for both Formulationon i.e Rasamanikya prepared by Kushmanda swarasa & Churnodhaka Shodita Haratala. The study aims to provide insights into the comparative efficacy and analytical aspects of these formulations for enhanced therapeutic outcomes.
Top 10 Best Ayurvedic Kidney Stone Syrups in India
Crowds Cure Canver: Annotating Data from The Cancer Imaging Archive
1. http://cancerimagingarchive.net
Justin Kirby – justin.kirby@nih.gov
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Informatics in Cancer Imaging (ICI) Team
Support to: Cancer Imaging Program/DCTD/NCI
Crowds Cure Cancer: Annotating data from
Citizen Science WG Meeting: Oct 2018
2. 2
The Cancer Imaging Archive: Brief intro
• 87 data sets (20 terabytes) consisting of
41,000 subjects (33 million radiology images)
• Covers radiology modalities (CT/MR/PET/RT)
and digitized pathology slides
• Wide variety of cancers + phantoms
• Patient populations vary from a handful to
>26,000 (NLST)
• Many have associated meta-data
Demographics/outcomes/therapy
Radiologist expert and automated
computational analyses (segmentations,
features)
• ‘Omics ties to GDC/TCGA, CPTAC, and GEO
http://www.cancerimagingarchive.net
3. 3
Tackling the de-identification challenge
PHI can appear in hundreds
of places in DICOM
• Dates
• Identifiers
• Descriptions
Potential legal risks are a
significant barrier to data
sharing for research
4. 4
TCIA services (not just software)
Relieves PI of majority of data sharing burden/risks
• Data hosting with >99% uptime
• De-identification using pre-configured RSNA’s Clinical Trials Processor (CTP) and
DICOM PS 3.15 Annex E standards
• Multi-tiered QC process inspects both DICOM headers and pixels for PHI and
integrity of data set
Phone/email support available for end users and submitters
Extensive documentation throughout the site
Exposure to a large community of researchers
• Increase visibility of your work, get more citations!
5. 5
TCIA Services: Staffing
TCIA Management at UAMS
Prior, Smith
Data Collection:
Programs
Bennett, Berryman, Billelo
Data Collection:
Research Collections
Jarosz, Stockton, Honomichl
Data Collection:
Pathology
Sharma, Birminam, TBD
APOLLO
(clinical/backlog)
Levine, Angelus, TBD
Clinical Trials
TBD
Infrastructure Support
Smith, Nolan, Dobbins, Tarbox, Tobler, Frund, Utecht, Brown
CIP ICI
Management
Freymann
Kirby
Sullivan
Cordeiro
Hill
6. 6
Organization of TCIA ecosystem
The
Cancer
Imaging
Archive
Data Collection Center
•Tools and staffing to support data
collection, curation, and de-
identification
Data Access
•Browse (home page)
•Filter/Search (Data Portal)
•REST API
•Analysis Data
Data Analysis Centers
•3rd party web sites or tools which
connect to TCIA’s API or mirror its
data
7. 7
Data Collection Center: Publish Your Data
Primary Data (radiology, pathology, clinical, etc) Analysis Results (derived from primary data)
Image credit: Hugo Aerts
8. 8
Data Collection Center:
Publishing data in addition to manuscripts
Data citations for both primary and analysis data to enable reproducible research
Analysis Dataset Citation (derived image features)
Gutman DA, Cooper LA, Hwang SN, Holder CA, Gao J, Aurora TD, Dunn WD Jr, Scarpace L,
Mikkelsen T, Jain R, Wintermark M, Jilwan M, Raghavan P, Huang E, Clifford RJ, Mongkolwat
P, Kleper V, Freymann J, Kirby J, Zinn PO, Moreno CS, Jaffe C, Colen R, Rubin DL, Saltz J,
Flanders A, Brat DJ. (2014). MR Imaging Predictors of Molecular Profile and Survival: Multi-
institutional Study of the TCGA Glioblastoma Data Set. The Cancer Imaging Archive.
http://doi.org/10.7937/K9/TCIA.2014.4HTXYRCN
Publication Citation (cites specific data used)
MR imaging predictors of molecular profile and survival: multi-
institutional study of the TCGA glioblastoma data set. Radiology.
2013 May;267(2):560-9. doi: 10.1148/radiol.13120118. Epub
2013 Feb 7. PubMed PMID: 23392431; PubMed Central PMCID:
PMC3632807.
Primary Data Citation (TCIA images used for study)
Scarpace, L., Mikkelsen, T., Cha, soonmee, Rao, S., Tekchandani, S.,
Gutman, D., … Pierce, L. J. (2016). Radiology Data from The Cancer
Genome Atlas Glioblastoma Multiforme [TCGA-GBM] collection. The
Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.RNYFUYE9
9. 9
Data Descriptor Journals
Journal Recommended Repositories
Nature Scientific Data https://www.nature.com/sdata/policies/repositories#imaging
Medical Physics http://aapm.onlinelibrary.wiley.com/hub/journal/10.1002/(ISSN)2473-4209/about/author-
guidelines.html (see section 13-Medical Physics Dataset Articles)
Elsevier Data in Brief http://www.elsevier.com/authors/author-services/research-data/data-base-linking/supported-
data-repositories#Health
PLOS ONE http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories
Research Data Support https://www.springernature.com/gp/authors/research-data-policy/repositories-bio/12327160
Publish detailed descriptions about how to use your TCIA data to gain
academic credit (publication/citations) in addition to the novel scientific
findings you might publish in traditional journals.
10. 10
Researchers want to share data – 38 data set queue
Community Proposed Data Sets
GBM-DSC-MRI-DRO
ASCC TNM Consensus
Colorectal Liver Metastases
QIN-BREAST-02
MyelomaTT3a
Low Dose CT Liver Metastases
Lung Fused-CT-Pathology
HNSCC Oropharyngeal Radiomics
OPC-Radiomics
Oropharynx Phantoms
HNSCC 3D CT RT
MSK Pancreatic Cancer Repository
Program Data Sets Notes
TCGA 2 collection//sites
CPTAC 9 cancer types, 14
sites
Exceptional
Responders
24 of 58 subjects
remaining
Immunotherapy 2 cancer types
PDX mouse Not started
NCTN integration RTOG 0617 pilot in
process
QIN ECOG-ACRIN 10 trials
12. 12
A significantly growing community!
38 incoming data sets in varying stages of curation
Over 10,000 active users per month
• Up from ~3,000/month in 2015
Downloads of 40-50TB per month
• Up from ~2TB/month in 2015
613 publications based on TCIA data
• 134 new publications in 2017
13. 13
Crowds Cure Cancer: The motivation
Continued growth: Engage researchers outside the medical
community
Computer science researchers often lack disease understanding
or sufficient contact with medical experts
Labeling basic information in the images such as tumor locations
to create “training data” can enable others to apply new methods
to our data
TCIA has this kind of annotation for some data sets, but not all
Performing such annotations/labeling using a small number of
radiologists is extremely time consuming and expensive
15. 15
TCIA Acknowledgements
University of
Arkansas
Dr. Fred Prior
Dr. Lawrence Tarbox
Kirk Smith
Bill Bennett
Tracy Nolan
Julie Frund
Sean Berryman
Dwayne Dobbins
Quasar Jarosz
Jeff Tobler
Sonya Utecht
Diana Stockton
Betty Levine
Erica Bilello
Geri Blake
Robert Brown
Leidos Biomedical Research, Contract 16X011
for NCI, Maintenance and Extension of The
Cancer Imaging Archive (TCIA ) (Prior)
NBIA Team
(NCI/FNLCR/Ellumen)
Ed Helton
Ulli Wagner
Scott Gustafson
Qinyan Pan
Russ Rieling
Carolyn Klinger
Martin Lerner
Tin Tran
Contractor
John Perry
Frederick National Laboratory
for Cancer Research (FNLCR)
John Freymann
Justin Kirby
Brenda Fevrier-Sullivan
Pam Angelus
Carl Jaffe
Luis Cordeiro
Craig Hill
Emory University
Dr. Ashish Sharma
Ryan Birmingham
17. Agenda
Background
Collaborators
System Development
General impressions from RSNA of the
experiment
• Feedback from participants
Current status/results
Features to be added
Next steps
18. Background
Annotated data is key to improving
performance of machine learning algorithms
Inter-rater agreement, even among experts,
can be less than optimal
• Helpful to have multiple annotations per case
Getting annotations is expensive
Hypothesis: crowd-sourced annotations, even
derived from non-experts, can be used for
machine learning
19.
20.
21.
22.
23.
24. Collaborators Erik Ziegler/Gordon Harris
(OHIF/MGH/ITCR)
Steve Pieper (ITCR)
Lawrence Tarbox, Jeff Tobler, Fred Prior
(UAMS/ITCR)
Ashish Sharma (Emory/ITCR)
Jayashree Kalpathy-Cramer/Artem
Mamonov (MGH/ITCR)
Justin Kirby, Brenda Fevrier-Sullivan, John
Freyman (FNL)
Erich Huang, Paula Jacobs (NCI)
RSNA (Informatics)
25. System
Architecture
TCIA
• Used images with known “truth”
from TCGA studies/Carl Jaffe
Azure VM
Cornerstone Viewer
• Lightweight version, mobile friendly!!
Chronicle DB (CouchDB) backend
• DICOM aware!
Registration system
• Logic for next case
JS/D3 for results (in progress)
• Charts
• Summary tables
26. General
Impressions
Overall seemed to be a success
Many participants ended up spending
more time than planned
Viewer was responsive
No major complaints about system
performance
Results are (very) promising
27. Logistics
Better location?
• Near case of the day
Coffee, water, cookies, chocolate
Wipes or alcohol wash for hands
Integration with RSNA app
35. Lung results y = 0.8574x + 5.0806
R² = 0.8379
0
10
20
30
40
50
60
70
80
0 10 20 30 40 50 60 70 80
Averagemeasurment
ground truth measurement
Comparisons to ground truth
36. Feedback
on interface
Need to start with a click through tutorial
Window/Level presets
Ability to change category mid session
• Also important when multiple cancer types are chosen.
Mobile support?
Flag button for quality with text box for comments
No log in when username is empty
Logout button
Need metrics - time per session, scores per session
People asked to see the number of cases they annotated somewhere on
the screen.
Add sagittal and coronal views for measurement accuracy
A few did not like the randomization of the images if they selected 3 or
4 cancer types – they complained about getting a bunch of all liver or all
lung cases at a time; and said they would have preferred being given
the options of which to do next.
System stalled if images for only one cancer type was selected and all
the cases were completed.
Reorder buttons – keep essentials only for mobile
Teaching interface – provide immediate feedback compared to
“consensus”?
Key up/down
37. Features to
be added
Annotators by type
Time histogram by type
Update charts to remove skips
Ability to all annotations for each case
• screen shots of all annotations
Statistics on variability of measurement
Ability to filter out by type??
• Can’t filter out our best annotator (misty_mandrill) but can’t
keep in junk?
Filter out by number of cases annotated
• If <5, probably just trying to see what it is all about
Compare to ground truth
• Add data for all cases
• Convert AIM measurements to cornerstone
Length, approximate slice
Ability to overlay all annotations including GT
38. Potential
next steps
for system • Permanently linked from TCIA
• Road show to various meetings?
• (Link to challenge platform)
Editor's Notes
Provide DOIs to collections and meta-collections (article’s analysis)
Publication can refer to the specific data sets used via the DOIs in the data citations
Currently working with NLM, collaborating with Nature Scientific Data and other publications