Utilization of virtual microscopy in a cooperative group setting


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Utilization of virtual microscopy in a cooperative group setting

  1. 1. 1Utilization of Virtual Microscopyin a Cooperative Group SettingThe Research Institute at NationwideChildren’s HospitalResearch Informatics CoreBiopathology CenterTom BarrBill BeyerDave BilliterAgendaOverview of the Biospecimen CorePurpose of Cooperative CancerGroupsPathological EvaluationElectronic PathologyMolecular Based MethodsMedicine for Gen XI
  2. 2. 2Research Informatics Core MissionThe Research Informatics Core of TheResearch Institute at NationwideChildren’s Hospital, under the visionof Dr. Stephen J. Qualman anddirection of Dr. Nilsa Ramirez, is aninformatics application developmentteam dedicated to increasing curerates and decreasing side effects intherapy through innovation ofinformation technology.Informatics Core TeamDave Billiter, PMP- Informatics DevelopmentManagerTom Barr- Imaging ManagerBob Neville- Senior Software DeveloperScott Hargrose- Software Developer/DBABill Beyer- Software Developer/Business AnalystHeather Bao- Software DeveloperHeather Day- Quality Assurance/Tech Writer/PMSubha Krishnamachary- Software DeveloperAndy Fox- Software DeveloperMark Plaskow- Software ArchitectEric Kramer- Data Architect
  3. 3. 3Informatics Core TechnologyMicrosoft .NET Framework (.NET Suite)MS SQL Server 2000/2005 (6.5/7)MS Access 97/2000/2003/2007MS Team Foundation ServerMySQLColdFusionJavaRuby/Ruby On RailsAperio ScanScope and Image SoftwareLinux/Apache/PHP/JSPFreezerworksBiopathology Center (BPC)Non-profit organization whose primaryobjective is the long-term acquisition andstorage of cancer-related tissues to supportcutting edge research (also normal andnon-cancerous tissue)Largest pediatric specimen bank in nationBegan accruing specimens in 1989Directed by Dr. Nilsa Ramirezhttp://www.biopathologycenter.org/
  4. 4. 4Biopathology CenterSpecimen Management Services for:Pediatric Cooperative Human TissueNetwork (pCHTN)Children’s Oncology Group (COG)Gynecologic Oncology Group (GOG)Childhood Cancer Survivor Study (CCSS)Clinical Trials Evaluation Program (CTEP)The Cancer Genome Atlas (TCGA)Strategic Partnering for the Evaluation ofCancer Signatures (SPECS)BPC by the NumbersOver 650,000 specimens currently in bankReceive tissues from over 500 hospitalsfrom the US, Canada, New Zealand, theNetherlands, Australia and Switzerland90% pediatric solid tumor cancer casesdiagnosed in US and Canada90% of the nation’s childhood leukemia casesReceive and process 100 cases or 500aliquots each dayDistribute over 25,000 specimens annuallyto over 130 academic and commercialresearchers
  5. 5. 5BPCOur function is to ensure the proper collection of, storageof, and access to, high quality well annotated humanspecimens, collected from representative patientpopulations and entered into NCI funded clinicaltreatment trials.Prepare specimen collection kits, receives specimens,prepares liquid samples, banks specimens (frozen, liquid,and paraffin specimens),Prepares nucleic acids, organizes pathology review,develops informatics systems and software to supportenriching the repository with easily tracked andretrievable inventory and clinical data, distributes tissue,and constructs tissue microarrays (TMAs)Biopathology Center ComponentsBiospecimen RepositorySpecimen management, quality control, expertpathology reviewCore MorphologyHistology servicesMolecular GeneticsHigh Throughput Genotyping and SequencingCoreALL Reference Laboratory for the COGDigital Imaging CorePerforms image acquisition of histologic slidesfor QC and review purposes
  6. 6. 6Digital Imaging CoreSupports multiple investigators andcooperative groups for pathologyreview including QC review of tissuequality and pathology review by theexpert pathologists to make certainthat the patients qualify for a specificprotocolEducationTechnology has been endorsed to improveturnaround time for rapid review and to train juniorpathologists in the review process.The goal is to employ Virtual Microscopy as Trainingand Educational Tool While Not Delaying TurnaroundTime for Protocol Diagnostic and Data ReviewPathology TrainingPathology Teaching Sets – rare tumorsDifficult Case ReviewsAllied Health fieldsBiology
  7. 7. 7ResearchIntegrating a virtual microscopy service into theresearch workflowSystems acts as a catalyst to advance collaborativepediatric and gynecologic pathology researchImage AnalysisImage WarehouseWhole slide images, gross images, radiology imagesSifting mechanism across multiple data sets toreturn data for specific users and diseases.Answers specific questions from differentperspectives.Pathology, computer science, biology, statisticianFurther research in image analysisNecrosis, Anaplasia & NeuroblastomaAgendaOverview of the Biospecimen CorePurpose of Cooperative CancerGroupsPathological EvaluationElectronic PathologyMolecular Based MethodsMedicine for Gen XI
  8. 8. 8Cooperative Cancer GroupFunded primarily by the National CancerInstitute (NCI)Large network of researchers, physicians,and health care professionals at public andprivate institutionsWork together to treat a large number ofpeople in the same way so that newtreatment can be tested quicklyTreatment ProtocolsTreatment instruction for a specificdisease and stage of that diseaseDefines requirements for pathologyreview includingmicroscopic visual examination oftissues, with special stains andimmunohistochemistry employed tovisualize specific proteins and othersubstances in and around cell
  9. 9. 9Children’s Oncology GroupOver 5,000 pediatric cancerspecialists located at 240 pediatricmedical centers in the United States,Canada and AustraliaOver 150 concurrent studies ofleukemia, brain tumors and the otherprincipal cancers of childrenOver 90% of pediatric cancer casesdiagnosed in US and CanadaGynecologic Oncology Group50 principal centers, most of which are academiccenters, and over 160 affiliate institutionsOver 2,100 gynecologic oncologists, medicaloncologists, pathologists, radiation oncologists,nurses, statisticians, basic scientists, quality oflife experts, data managers, and administrativepersonnelOver 3,300 patients are registered each year toGOG research trialsTo date, GOG has completed over 300 clinicaltrials and contributed over 550 manuscripts tothe peer reviewed medical literature
  10. 10. 10AgendaOverview of the Biospecimen CorePurpose of Cooperative CancerGroupsPathological EvaluationElectronic PathologyMolecular Based MethodsMedicine for Gen XI
  11. 11. 11Pathology ReviewProvide expert pathology review to ensurecorrect diagnoses of case material forprotocol assignment, clinical and biologicalcorrelative studies and tissue bankingThere is an appreciable misdiagnosis rateby local pathologists (20 to 40%),underscoring the value of review prior toprotocol enrollment and entry ofbiospecimens into the tumor repositoryAgendaOverview of the Biospecimen CorePurpose of Cooperative CancerGroupsPathological EvaluationElectronic PathologyMolecular Based MethodsMedicine for Gen XI
  12. 12. 12Digital PathologyThe technique of digitizingmicroscope slides with commonobjective magnificationsEquivalent to original glass slides onmicroscopesProvides diagnostic image qualityDigital Images may be more valuablethan glass slides…..Caveats of Digital PathologyIntroduction of a new technology toan established work groupCosts associated related to imagescanners, hardware (storage), andsoftware (management)Limitations in the technologyImage sizeBandwidth requirementsScan times
  13. 13. 13Benefits of Digital PathologyReproducible diagnosis as comparedto glass reviewsEliminates distribution of glass slides,logistical issues with rapid turnaroundtimes, and costs of tracking and lostor broken slidesSupport image analysisBetter quality than static imagesAccessible anytime via the InternetWhy Digital Pathology?Improve patient care by reducing reviewtimesReduces use of precious research materialReduces costs associated with cuttingmultiple slide sets, shipping costs, brokenglass slidesAccessible anytime via the InternetEducational Potential much improved overtraditional teaching setsSupport image analysisEasy retrieval of pathology images
  14. 14. 14Digital Pathology Business ProcessA significant achievement has beenthe coordination of central pathologyreview using virtual microscopy.Imaging HardwareAperio ScanScope XT (2)Viewing Station in AnatomicPathologyNAS Device – 1 Tb6 Tb local storageclusterVirtual SlideRepository
  15. 15. 15Pathology Review WorkstationIndustry Partners10 Tb storage cluster at the OhioSupercomputer Center (OSC)Serve images from the OSCGB connectionBeta testing site for AperioOSC HPCMicrosoft Life Sciences
  16. 16. 16Evolution of the TechnologyCreate digital slidesof blood smear,bone marrow,Gram stain, andother specimensusing oil immersionon the ScanScopeOS SystemCommercial SoftwareSSH Communications Security SSHMathWorks MatLabAperio ImageScopeAperio ImageServerAperio WebViewerAperio Digital Slide ConferencingAperio Digital Slide StudioAperio SpectrumPlus
  17. 17. 17Custom Application DevelopmentVirtual Pathology Image Analysis withthe Image DashboardDVD HTML GeneratorScanner Scheduling SystemVirtual Microscopy Request SystemVIPERVM2MImage DashboardSlide processor for cancerousdiseasesAllows users to query multiple imagesby morphologic characteristicsAlgorithms to detect and measurenecrosis, anaplasia & mitotic index
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  20. 20. 20Virtual Imaging for Pathology,Education, and Research (VIPER)Web-based pathology review system thatis extensible both for today andtomorrow’s research needsFacilitates a more efficient and cost-effective pathology review process ofpatient tissue submitted by memberinstitutionsIntegration of a virtual microscopy serviceinto the research workflowActs as catalyst to advance collaborativepediatric and gynecologic pathologyresearch and research in image analysis
  21. 21. 21Expert Reviewers and VIPEROnline registration andrequest for passwordresetsNotified via email ofnew casesPersonalized screenwith list of cases andcase status afterauthenticating intoVIPERSystem monitors newcases, completedcases, and casesunder reviewAbility to annotateimagesOnline forms forcompletionEmail notification ofcompleted cases to theBPCUser’s manualavailable onlineBPC Operations and VIPERAssign PasswordAssign Cases and/orgroups of casesUpload PathologyReportsAdd Staff AccountsAdd or RemovereviewersManage CasesManage SlidesManage GroupsManage InstitutionsQuery for Case statusby reviewer or protocolImage DirectoryAssignmentOnline User’s Manual
  22. 22. 22VIPERVIPER
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  25. 25. 25VIPER G3In Development by the ResearchInformatics CoreAbility to connect to multiple imagedata centersVoice recognition for online formsOnline chat for Digital SlideConferencingAlgorithms for Image Quality
  26. 26. 26Rich Image WarehouseCurrently populated with whole slide pathology imagesSupplement current image set with additional imagetypes (radiology, cardiology, etc.) and correlatedmetadataSupports sifting through multiple data sets to returndata for specific users and diseases providing data toanswer specific questions from different perspectivesPathology, computer science, biology, statisticianFurther development of analysis algorithms for multipleimage typesSynergistic personalized healthcare medicine throughexpert systems and decisioningIntegration with Personal Health Records/ElectronicMedical Record/Laboratory InformationSystems/Radiology Information Systems facilitatingpersonalized medicineAgendaOverview of the Biospecimen CorePurpose of Cooperative CancerGroupsPathological EvaluationElectronic PathologyMolecular Based MethodsMedicine for Gen XI
  27. 27. 27Virtual Microscopy to Microarray(VM2M)Creates a system where Virtual Microscopy datais made available alongside microarray data fordisease diagnosis and treatmentWeb-based system where a pathologist cansearch for tissue samples of interestReviewer can inspect the corresponding digitalimage using a web based image viewer, with theability to zoom and pan to the desired parts ofthe imageReviewer will also have the ability to access themicro- array data corresponding to the sametissue sample, along with results from anautomated analysis of the digital image
  28. 28. 28VM2M AccomplishmentsCompletion of first iteration, whichincludes the biology and molecularcomponents of a COG IRSG (Rhabdo)study.192 cel files; 146 imagesComplete framework designed anddeveloped in a secure and flexiblemethod, which allows for addition offuture components (e.g. Radiology).
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  32. 32. 32AgendaOverview of the Biospecimen CorePurpose of Cooperative CancerGroupsPathological EvaluationElectronic PathologyMolecular Based MethodsMedicine for Gen XIVM2M G3A clearer strategy for the development of novelstrategies for high-risk disease, demonstratingthe links between molecular pathology andtherapyIncrease number of studies with correspondingbiology and molecular dataIncorporate Electronic Lab Notebook functionalityAdd additional components to the framework ofthe application (Radiology, Proteomics, etc.)Increase overall search capabilities, reporting andexport functionality, and other added features
  33. 33. 33High Dimension Data AnalyzerA web-based, patient-driven,dashboard application whichintegrates data from disparatemodalities, applications and datasources at one single point of entry.AcknowledgementsAperio TechnologiesChildren’s Oncology GroupGynecologic Oncology GroupMicrosoft Life Sciences DivisionNationwide Children’s HospitalOhio Supercomputer Center
  34. 34. 34QuestionsOpen DiscussionThomas.Barr@NationwideChildrens.orgBill.Beyer@NationwideChildrens.org