Management of spatially organized biological data using EMAGE

Abstract

Images are used to record the outcomes of many biological experiments, including those that employ in situ hybridization and immunohistochemistry assays. The most widespread method currently used to describe these images for archiving and analysis purposes is employing a text based description, whereby the pattern of staining observed in each image is described by a human using a standardized vocabulary of anatomical terms. In this chapter, we describe a complementary approach, whereby, the spatially organized information inherently contained in data images is extracted and spatially integrated via a semi-automated process and then housed in a three-dimensional atlas of biological structure. Thus, spatial data from multiple assays can be interrogated directly by spatial based approaches to find patterns that display similarities or differences of patterns over local or entire regions of the specimen.