Analysis of gene expression by in situ hybridization (ISH) provides high-resolution information reflecting both gene expression level and location within a tissue or even full organism. ISH can be automated, thereby enabling the determination of gene expression patterns for thousands of genes (large scale ISH). Whole-mount embryos or tissue sections are placed and fixed on a standard microscope slide (A, B). DNA templates are transcribed to cRNA strands, termed riboprobes, which are hydrolyzed, labeled and hybridized to the sections (C). The riboprobes hybridize to their complementary RNA transcripts in the sample, thereby enabling visualization of the RNA transcript location (D).