Overview

This is a collection of analysis tools to study RNA localization from single molecule FISH (smFISH) images. These tools were developed in the context of RNA localization in liver, but can likely be applied for different questions as well.

We provide different analysis workflows (listed in the banners above ). For each we specify the required installations, and detailed Instructions for how run these workflows and what results are typically obtained.

General analysis workflow

1. The tools require a very specific data organziation that we specify
2. RNA detection is performed with FISH-quant in Matlab.
3. Post-processing is performed with ImJoy plugins.

ImJoy plugins

Most of the workflows are implemented as ImJoy plugins, with a simple interface to specify the different workflow parameters. We describe in a dedicated section how to use ImJoy and the Plugin engine to run these plugins.

Quick summary for how to connect ImJoy to Jupyter engine

1. Open anaconda terminal.
2. Activate environment: conda activate rna-loc-liver
3. Start Jupyter engine: imjoy --jupyter
4. Connect ImJoy to Jupyter Engine with 🚀 button.

We also provide Jupyter notebooks for these workflows, which we recommend only for more experienced Python users.