The Stanford Tissue Microarray Database

Abstract

The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. As of July 2007, TMAD contained 205 161 images archiving 349 distinct probes on 1488 tissue microarray slides. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. To date, 12 publications have been based on these raw public data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Image processing researchers can extract images and scores for training and testing classification algorithms. The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license.

Figure 1.

Each tissue microarray contains hundreds of tissue samples. TMAD provides tools to assist the histologist in selecting tissues by parametric search as well as by providing batch upload of new de-identified tissue metadata.

Figure 2.

Tissue microarray workflow: using TMAD-specific microarray block(s) are selected for an experiment. Slides are cut from the tissue microarray and antibodies are used to visualize protein expression or in situ probes to visualize DNA and RNA targets. The results are imaged on bright-field or fluorescence automated microscopes with results uploaded and archived in TMAD. Pathologists may annotate and score manually or online with results saved for analysis in TMAD.

Figure 3.

TMAD query and analysis tools: tissues and stains are selected by browsing or parametric search, replica spot scores are collapsed and intermediate files are produced for optional download. Data can be clustered, the resulting heatmap visualized and summarized with annotated thumbnail images. Full resolution tissue images are always available by clicking any thumbnail.