Abstract: Disclosed are methods permitting colonies of nucleic acids produced by amplifying them in an immobilized medium to be visualized with a homogeneous fluorescence detection system which is introduced into the medium before amplification. No post-amplification steps, such as opening the gel, blotting, hybridization, and removal of unbound substrates, dyes, or probes are needed, and the growing molecular colonies can be monitored in real time. Also disclosed are methods for quantitative in situ assays of nucleic acids contained in individual cells or in tissue fragments. The methods are conveniently executed using a disposable transparent chamber containing dry matrix of the medium and equipped by inlet and outlet ports that serve for filling the chamber with a solution comprising components of amplification and detection systems, said solution being absorbed by said matrix to swell all over the inner volume of said chamber.