tissue micro-array databasedemarzolab.pathology.jhmi.edu/docs/onc_meeting.pdf · james d. morgan*...
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TMA-J
Dennis Faith Brian Razzaque*
James D. Morgan*Helen Fedor
Angelo M. De Marzo
Open Source Software to Manage a Tissue Microarray Database
*VMT LLC.
Slide from Mark A. Rubin, M.D., U. Michigan
Tissue Microarray – 400 cores, 0.6 mm each
Tissue Microarray – 400 cores, 0.6 mm each – H&E of 4 µm section
Need for Data Management
200 TMAs from Johns Hopkins TMA lab
What is TMA-J?• TMA-J is a set of open source software tools
and backend database structure to facilitate management and analysis of tissue microarrays and associated pathology and image data
What Does TMA-J Do?
The Database Tracts:• Clinical information about patients (currently
limited)• Pathology specimens and associated data• Pathology tissue blocks • Tissue Microarray cores• TMA Blocks• TMA Slides• TMA core images• TMA image scoring data: manual or semi-
automated
What Does TMA-J Do?
• Entering pathology data• Managing users and permissions• Designing TMAs• Viewing and scoring TMA (and other) images
online• Viewing multiple TMA images from the same
spot• Publishing TMA images and datasets on the
WWW
The software applications provide a platform for:
Original Database
• The original database used Microsoft Access and the code was written in Visual Basic
• All users had full access to the database• Patient identifiers were not isolated or encrypted• Data was specific to the prostate • Applications could not be accessed over the web
Primary Goals of New System• Address security concerns• Remove or isolate patient identifiers • Manage multiple organ systems• Web accessible • Scalable to accommodate large number of
simultaneous users• Storage of large sets of images with
diagnoses • Data structure compatible with emerging
standards for easy data exchange
Database Design
.
Specimens Table
• Represents a specimen from surgical pathology.• Key fields
*SurgPathNumber*SpecimenTypeID*PatientID*Hospital*Physicians
• Since specimens is a “dynamic” table, fieldnames for different organ systems can be added. For example, we could add a “Gleason Score” field for the prostate, and Elston Grade for breast.
Blocks Table
• Represents a paraffin block cut from a specimen
• Fields:* BlockID * SpecimenID * Part number * Designation
TissueDiagnosis Table (Sub-Block)
• A Tissue Diagnosis represents a sub-area of a donor-block with a diagnosis (e.g. cancer)
• Fields* TissueDiagnosisID * BlockID* LesionLetter * TissueTypeID
• Since tissue diagnosis is a “dynamic” table, fieldnames for different organ systems can be added. For example, we could add a “ProstateZone” field for the tissue type “Prostate –Cancer”
ArrayCores Table
• Represents a cylinder of tissue taken from a donor block, and then placed into a position (e.g. x=3,y=5) in a recipient Array Block.
• Fields*ArrayCoreID *ArrayBlockID* X *Y* Control *TissueDiagnosisID
Security
Security: Protecting Patient Information
• Database stored on a secure server• Identifiable patient information in encrypted
tables (Approved by the IRB)• Researchers have no access to patient
identifiers• Creates virtual separate entities: “clinical
database” and “research database”
Security: Separation of User’s Data
• Users can share or separate their data based on study and sample permissions
• Permissions can securely limit access to specific specimens, blocks, array-blocks, and sessions
DATA
Tissue Microarrays 341
Array Cores 49785
Specimens 15757
Blocks 10186
Array Slides 444
Array Core Images 74081
Users 104
Applications & Screenshots
Applications – Java from Sun Microsystems
• All Applications are Written in Java for Cross Platform Compatibility
Java Web Start Software
• Allows users to download and run Java applications from the web.
• One-click activation of applications • User is always running the latest version of the
application • Eliminates complicated installation or upgrade
procedures • Highly-interactive user interface • Built on top of the Java 2 platform, which
provides a comprehensive security architecture
http://java.sun.com/products/javawebstart/architecture.html
Applications
http://tmaj.pathology.jhmi.edu/
Data Input Application• This application allows for detailed input of data on
individual specimens and donor-tissue-blocks.
ArrayBuilder Application• The ArrayBuilder application allows users to design Tissue
MicroArrays.
Import Application
• Imports array images from a scanning system such as Bacus lab’s BLISS or Chromavision’s ACIS II, as well as the autoscored data
• Imports specimens from a tab-delimited file Alternatively, specimens can be entered manually
Tissue Microarray Image Acquisition
• Tissue MicroArray slides are scanned using the Bacus Laboratories Inc. Slide Scanner (BLISS) and Chromavision Automated Cellular Imaging System (ACIS)
BLISS ACIS
Images Application
Image Application: Filtering• The table shows information about every image (identified by x
and y) in an ArraySlide. • Images identified as “Prostate – Carcinoma” are highlighted in red.
Images Application: Viewing 2 Stains
Image Quantification - Example
020
4060
8010
0TF
F3 V
isua
l Dat
a/Fi
tted
valu
es
0 20 40 60 80 100TFF3 Automated Data*
r = 0.9165n = 182
Publishing TMA Images and Scoring Data Over the Internet
• Roughly modeled after Stanford Microarray Database
• Concept:• Once a study is published by a journal, all
tma diagnoses, image, scoring and non-protected clinical data can be “published” as supplemental data to the internet for public online viewing or down loading
Security – Individual Scanned Array Slides
• Users can:• Share image scoring sessions with
specific users• Finalize image scoring sessions• “Publish” finalized scoring sessions for
public viewing over the Internet
For More Information
• http://tmaj.pathology.jhmi.edu• To see published images
• Click on the “Images” application and login as• Username: guest• Password: guest
• Selected Lab Publications• http://demarzolab.pathology.jhmi.edu/De_Marzo_Laboratory_Interests_and_Publications.html
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