Overview of TMAJ

What is TMAJ?

TMAJ is open-source software that provides ways to store and retrieve information related to tissue micro-arrays.
TMAJ was created by the Johns Hopkins TMA Core Facility. The J in TMAJ refers to Java, as TMAJ is programmed 100% in Java.

Data Stored in TMAJ

TMAJ allows the storage of a wide variety of information related to TMA samples, including:

Images on the ArraySlide
Patients
Specimens
Donor Blocks
Array Cores
Array Blocks
Array Slides
Machine-Scored Data
Image Analysis Data

Dynamic Database Structure

One of TMAJ's most powerful features is its dynamic database structure. This allows users with administrative access to add custom fields for different organ systems. For example, a group studying prostate cancer will record different data than another group who studies colon cancer. With this structure, an administrator can have multiple organs, with each organ having its fields. For example, a prostate type may have a field called "Gleason Score". TMAJ provides an application that allows an administrator to add, change, or delete these fields. Administrators may also assign what choices a field may have. For example, an administrator may assign the field "Primary Gleason Score" choices "1", "2", "3", "4", and "5".

A screenshot from the Images Manager application in TMAJ. In the above image, the user chooses the type "Prostate -- Carcinoma". Based upon this choice, certain fields and choices are displayed in the table. In the above image, the field displayed is "Primary_Histologic_Type". One of its choices is "Prostatic Adenocarcinoma, Gleason 3, Non Cribriform". This field and choice are only displayed when the user chooses the "Prostate -- Carcinoma" type. If the user would have chosen the "Bladder" type, this choice would not have been displayed.

A screenshot from the Meta Data application in TMAJ. The Meta Data Application allows an administrator to determine which types (e.g. prostate, bladder, etc) TMAJ will contain, and what fields each type will have. For example, the "prostate" type may have a "Prostate_Zone" field, whereas this would be irrelevant for a "bladder" type. Additionally, each field may have choices associated with it. In the above example, we see the "Prostate Zone" field has choices such as "Central Zone" and "Peripheral Zone".

Data Security & HIPPA

TMAJ has extensive security features, as it was designed with HIPPA legislation in mind. These security features are default with a new TMAJ installation, and can be fine-tuned by an administrator. All users in TMAJ are assigned a username and password and are required to log on to perform various functions. One of the main types of protected data is patient information. This includes protected patient data such as birth dates and names, as well as limited-data-set identifiers such as surgical pathology numbers. A TMAJ administrator may decide to deny all all access to patient information outright, or may allow access to a subset of specimen records. Access to other data types can also be tightly controlled by an administrator. These other data types include blocks, array-blocks, array-cores, array-images, array-slides, image-analysis data, and meta-data. Different levels of data-access may be provided, such as providing write access and read-only access.

TMAJ also supports a concept of group-administrators, who have adminative rights over a subset of users. Group-administrators control only a subset of TMAJ data, and may assign privileges to this data to the subset of users they control.

Image Analysis

TMAJ has capabilities for performing automated image analysis. This was done by integrating the Frida image analysis package.

Applications of TMAJ

TMAJ has 5 major applications:

SpecimensManager -- Used to enter data about Patients, Specimens and Donor-Blocks
ArrayBuilder -- Used to design ArrayBlocks
ArrayManager -- Used to enter information about ArrayBlocks, ArraySlides, & Scans
Import -- Used to import ArrayImages from a Scanning Machine (like the BLISS or ACIS).
ImageManager-- Used to score Images on an ArraySlide and perform image analysis.
Meta Data -- Used to add custom data fields to TMAJ.
Administrator -- Used to set security options

Overview of Technology Behind TMAJ

The client uses the server in 2 different ways:

To read or write information to the database
To get an image file from a Tissue MicroArray

Clients can read or write information to the database by first contacting the Apache Tomcat server. TMAJ has a Java servlet running on Tomcat. The client sends a Request class to the Tomcat servlet and receives a Response class back. In the Request class, the client places a username and password. Tomcat then returns a Response back to the client based upon the permissions of the person's user account. This Response class contains information from the database. By requiring each Request class to have a username and password, we can ensure that users only see information for which they have been assigned access.

If the client sent a Request class which asked Tomcat to write information to the database, the Response returned may only indicate if the data was written successfully or failed. Users are prevented from overwriting data to which they do not have access.

The Java servlet connects to the database using JDBC (Java Database Connectivity). The TMAJ database may be your choice of MySQL, Microsoft SQL Server, Oracle, or Sybase.

Image files are created by a technician using a scanning machine. TMAJ supports the ARIOL from Applied Imaging, the BLISS from Bacus Labs, the ACIS from Clarient (formally called ChromaVision), and the ScanScope from Aperio Technologies. A technician scans an array-slide, and the scanning machine converts each spot on the array-slide into a jpeg image file.

How the TMAJ client and server interact, and the technologies behind them.

Authors

TMAJ was created by Dr. Angelo De Marzo, Dennis Faith, and Helen Fedor of Johns Hopkins University, and James Morgan, Brian Razzaque, and Joe Zimmerman of Vision Multimedia Technologies (VMT).

License

TMAJ is open source software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

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