smFISH FAQ
If you are interested in getting started with single molecule RNA FISH yourself, check out our FAQ. It has a lot of information and answers to many common questions.

StarSearch (currently down: we are working on this!) and rajlabimagetools
Typically, both of these work well for counting spots in your images. While StarSearch is a more user-friendly application, it is currently out of service. In the meantime, please use rajlabimagetools, which includes a more extensive set of tools but requires some MATLAB familiarity.

protocols.io
Here you can find some of our protocols!