tissue micro-array databasedemarzolab.pathology.jhmi.edu/docs/onc_meeting.pdf · james d. morgan*...

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

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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