RNA localization in smFISH images

This is a collection of analysis tools to study RNA localisation from smFISH images.

We provide different analysis workflows (you can select them from the banners). For each we detail the tools and their installations.

We use a number of different open-source software packages, when necessasry we detail how to install them.

• RNA detection is performed with the Matlab package FISH-quant (more details below).
• Most postprocessing steps are performed with Python plugins running ImJoy. To use them, you have to install Python with Jupyter and the necessary ImJoy plugins. For more details see the respective sections below.
• Some annotation tasks are performed with Fiji, which you can download from here.