The first project of its kind to propose/create a “standard” means of adding information /knowledge to an image in a clinical environment in order to create a future in which image content can be easily and automatically searched. AIM provides a solution to the following challenges:

• No agreed upon syntax for annotation and markup.
• No agreed upon semantics to describe annotations.
• No standard format (DICOM, XML, HL7, etc.) for annotations and markup.

iPAD Annotation Tool
A new tool developed by the AIM team to compliment the core AIM product. iPAD is used for radiology images, created as a plug-in to the popular OsiriX Open Source image viewing workstation. It implements the AIM standard (Annotation and Image Markup) of the caBIG project. iPAD also supports the RadLex controlled terminology for describing anatomic entities and observations in images. The purpose of iPAD is to make the semantic content (the meaning and other key metadata in the images) explicit and machine-accessible for query and data mining.

Bioconductor is an established open-source collection of software packages for high throughput genome analysis. Packages adapted for caBIG allow preprocessing of microarray data, DNA copy number assessment from gene expression data, and SELDI-TOFF mass spec peak finding.

caB2B is a caGrid client that permits scientists to leverage caBIG^TM compatible data services through a user friendly GUI.  A metadata-based query interface enables end user to search virtually any caGrid data service.  The ultimate goal of the tool is to aid translational researchers in combining data from tools like a caBIG^TM biospecimen repository service, caTissue Core/Suite, with data from a microarray data repository like caArray and use the analytical services to analyze and visualize the results.  caB2B has two modules, the administrative module and the end user client. 

The administrative module of caB2B is a GUI where the administrator can customize a particular instance for end users.  For example, an administrator can select models and service instances that may be queried, curate paths between classes in models, and create joins across models or applications. 

The end user client is a Java application that enables end users to query for and persist data available on the caGrid.  It also allows for the analysis and visualization of this information.  The query component consists of a diagrammatic view that allows the user to create a directed acyclic graph of the query that is to be executed and also helps the user to connect two or more classes to be searched.  The data obtained from the query may be saved as a ‘virtual experiment’ and analyzed further.  The end user may also visualize data in the experiment by using various graphical components.  Thus, caB2B is a caGrid client capable of querying and analyzing available data on the caGrid.  The complex combinatorial, visual, and statistical analyses that it currently enables and will facilitate in the future will result in a better understanding of the complex pathophysiology of polyfactorial diseases and will accelerate the identification of potential diagnostic markers and therapeutic targets for these illnesses.

The intent of caELMIR is to provide the pre-clinical scientist with a data management system to record experimental data. caELMIR is a “LIMS” system for basic scientific data.

caIMAGE is a cancer images database maintained by NCI. Investigators can register on the site, and then search for and submit images to the online image repository using a web browser. caIMAGE utilizes anatomy and disease vocabularies served by the NCI Thesaurus, a knowledgebase containing the working vocabularies for clinical, translational and basic research used in NCI data systems.

caIntegrator is a novel translational informatics platform that allows researchers and bioinformaticians to access and analyze clinical and experimental data across multiple clinical trials and studies. The caIntegrator framework provides a mechanism for integrating and aggregating biomedical research data and provides access to a variety of data types (e.g. Immunohistochemistry (IHC), microarray-based gene expression, SNPs, clinical trials data etc.) in a cohesive fashion.

caMicroscope is a remote viewing application for accessing grid enabled repositories of large pathology images. The project includes a caGrid data service, called the Pathology Data Service. Pathology Data Service currently supports the storage and region-of-interest (ROI) retrieval of pathology images acquired using the Aperio whole slide scanner and stored in Aperio’s SVS image format. The project also includes a grid-client, called caMicroscope, which can interact with the Pathology Data Service to interactively retrieve and display ROIs within the whole slide image. The user has the ability to pan through the image, select the size of their ROI, and select a zoom level.