De Marzo Laboratory

in the Johns Hopkins Department of Pathology

jhu logo


TMAJ is open-source software designed to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Frida was added to TMAJ, and thus TMAJ now supports image analysis.


Telomeres shorten in cancer and pre-cancerous lesions, therefore, the measurement of telomere lengths in situ will facilitate studies on cancer pathogenesis. To overcome the limitations posed by traditional Southern-based methods, we recently developed a technique for telomere length analysis in fixed tissue samples. In this method, quantitative data can be extracted using existing digital image analysis software. However, several of the image processing steps are cumbersome, requiring extensive manual intervention. We therefore have developed a custom software plugin for extracting telomere length data from fluorescence images using the analysis program ImageJ. This software streamlines the process of quantitative telomere length analysis and allows for direct export of results to an established MS Access database.


Frida is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility in conjunction with Toby Cornish, MD PhD. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH's ImageJ application. Note that Frida was recently added to TMAJ, and you should use TMAJ to get the latest functionality from Frida.

Color Deconvolution for TMA images

This is a collection of ImageJ macros (scripts) for performing color deconvolution and analysis of immunohistochemistry (IHC) staining on tissue microarray (TMA) images. The software was developed by Toby Cornish.