# Presentation: 710692

## TmaJ 

- Dennis Faith
- Brian Razzaque
- James D. Morgan
- Helen Fedor
-  Angelo M. De Marzo

- Open Source Software to Manage a Tissue Microarray Database

**Notes:**
Brian, please put this as the first slide

## What is TmaJ?

*TmaJ* is a set of software tools to allow seamless management and analysis of tissue microarray data and microscopic images

## What Does TmaJ Do?

- The Database Tracts:
- Clinical information about pathology specimens
- Pathology tissue blocks
- Tissue Microarray cores
- TMA Blocks
- TMA Slides
- TMA core images
- TMA image scoring data: manual or semi-automated

**Notes:**
These tools should facilitate analysis of immunohistochemical and in situ hybridization studies of gene expression in basic research,  prognostic studies, and for therapeutic monitoring.

## What Does TmaJ Do?

- Entering pathology data
- Designing TMAs
- Viewing and scoring TMA images online
- Viewing multiple TMA images from the same spot
- Controlling access by managing users and projects

- The software applications provide a platform for:

## Primary Goals of System

- Address security
- Flexible support to manage multiple organ systems
- Web accessible for multiple simultaneous users
- Scalable to accommodate large number of simultaneous users
- Store unlimited amount and types of clinical data and pathology data
- Storing of large sets of images with diagnoses and scoring data across organ systems
- Data structure compatible with emerging standards for easy data exchange
**The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data. J. Berman et al., (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=165444)**

## Slide from Mark A. Rubin, M.D., U. Michigan

**Notes:**
The TMA consists of cylindrical paraffin embedded tissue cores that are acquired from primary “donor” blocks. The donor block is a standard tissue block that may be from surgical pathology, autopsy or research material.  A morphologically representative area of interest within the donor block is identified under the microscope using a stained section (usually Hematoxylin and Eosin stained) on a glass slide as a guide.  The tissue cores are removed from the donor and inserted into a “recipient” paraffin block using a custom patented instrument from Beecher Instruments. Using a precise spacing pattern, tissues are inserted at high density, with up to 1000 tissue cores in a single paraffin block.  Sections from this block that are cut with a microtome are placed onto standard glass slides that can then be used for in situ analysis.  Depending on the overall depth of tissue remaining in the donor blocks, tissue arrays can generate between 100 and 500 sections. Once constructed tissue microarrays can be used with a wide range of techniques including histochemical staining, immunohistochemical/immunofluorescent staining, or in situ hybridization for either DNA or mRNA.

## 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**

## Database Design

## Slide 9

## .

**.**

**Notes:**
This one needs to be updated since we do not have tissue type at the block level anymore. 

## Security

## Database stored on a secure server (Windows 2000)
Identifiable patient information is stored in the database within an encrypted table (Approved by the IRB)
Researchers have no access to patient identifiers
Only those authorized by the IRB have access to the codes to decrypt the patient table
This creates virtual separate entities: “clinical database” and “research database”

- Identifiable patient information is stored in the database within an encrypted table (Approved by the IRB)
- Researchers have no access to patient identifiers
- Only those authorized by the IRB have access to the codes to decrypt the patient table
- This creates virtual separate entities: “clinical database” and “research database”

- Security: Protecting Patient Information

## Security: Separation of User’s Data

- Security is enforced through permissions protected by passwords assigned to users
*TmaJ* allows users to either share or separate their data based on study and sample permissions
- These permissions can in turn be used to securely limit access to specific specimens, blocks, array-blocks, and sessions

## Applications & Screenshots

## 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.
- Imports specimens from a tab-delimited file.  Alternatively, specimens can be entered manually.

## 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

## Administrator Application

- Allows administrators to limit data access.
- Allows administrators to modify information about users, array-blocks, array-slides, and protocols.

## Security Options: ArrayBlocks

- An administrator can control which ArrayBlocks a user can change.

## Security Options: Specimens

- Specimens may be assigned a study.  In turn, users may be assigned to one or more studies.  Thus, an administrator can control which specimens a user can access.

## Security Options: Images

- A project is a collection of ArraySlides.  Users are assigned to projects.  The end result is that an administrator can control which ArraySlides a user can view.

## For More Information...

- Visit _[http://tmalab.jhmi.edu](http://tmalab.jhmi.edu/)_ (about our TMA lab, with links to software)
- Visit http:
- View the Images Application
- Log on to _[http://](http://www.tmaj.com/)__[www.tmaj.com](http://www.tmaj.com/)_
- Install Java Web Start
- Click on the “Images” link
- Log in as Username: **guest** Password: **guest**
- Click on “Published Sessions” (session data can be viewed but not modified).
- Click on “Angelo De Marzo”
- Click on any of the available sessions