Can I use a confocal microscope with Stellaris RNA FISH probe sets?

We recommend the use of wide-field fluorescence microscopes as an entry point for researchers new to Stellaris and microscopy. However, more advanced microscopists have successfully employed confocal microscopy for imaging their Stellaris RNA FISH assays. Confocal microscopy uses point illumination to limit the focal plane for imaging. While this technique restricts light that is out of focus, it also diminishes the sensitivity of low-light level imaging.

To best detect individual transcript molecules, we encourage the use of conventional wide-field fluorescence microscopes with a 60-100x, 1.3 NA or greater, oil-immersion objective and a cooled CCD camera. The light source should be a mercury or metal-halide lamp (e.g., ExFo Excite, Prior Lumen 200). We recommend starting with a 1 second exposure time. Check out our blog article for tips on imaging Stellaris RNA FISH assays.