Luciferase seems more convenient. Why and When should I use NIS?

Luciferase is an excellent reporter gene for ‘quick and dirty’ studies of cell or virus fate in SCID or nude mice. Up to five mice can be imaged at one time making luciferase an excellent screening tool, and small numbers of cells can be detected, but images are two-dimensional and resolution is poor.

Importantly, researchers from the University of Minnesota recently reported that firefly luciferase is immunogenic, resulting in substantial loss in gene expression levels in immunocompetent mice over time. Hence, luciferase is not desirable for long term cell tracking studies. 

Reference: Cellular immune response against firefly luciferase after sleeping beauty-mediated gene transfer in vivo. Podetz-Pedersen KM, Vezys V, Somia NV, Russell SJ, McIvor RS. Hum Gene Ther. 2014 Nov;25(11):955-65. doi: 10.1089/hum.2014.048. Epub 2014 Sep 22. PMID:25093708