RNA detection in smFISH images with ImJoy

This repository contains code for graphical user-interfaces powered by ImJoy to analyse smFISH images with our Python analysis package big-fish.

Getting started.

  1. Read this documentation.
  2. Install the ImJoy plugin engine (we explain what this is just a bit further down).
  3. Install the FISH-quant plugins.
  4. Try to analyze the provided test data either with our interactive documentation (see below) or a local installation.

ImJoy? Big-FISH? Plugin engine?

There are a number of different components that work together, which might be a bit confusing. Below you can find a smaller overview, they will be presented in more detail in the documentation:

q-imjoy-overview.png

There are three essential parts:

  • ImJoy: ImJoy is a plugin powered computing platform to deploy advanced image analysis tools. FISH-quant is implemented as a set of such plugins. Plugins can be installed with a simple installation link. More details about ImJoy and how it can be installed, can be found in the decicated overview section.
  • Plugin Engine: the ImJoy app is running in your webbrowser (prefereably Chrome) and provides the user-interface. In order to perform computations, you have to install the so-called plugin engine which runs Python (only once). When you use FISH-quant, you have to launch this engine and can connect ith with ImJoy.
  • big-fish: Python code performing the actual analysis (available in a dedicated GitHub repository. This package can be used to build your own analysis pipeline, but here we provide convient user-interfaces implemented in ImJoy for the most common tasks.

Interactive documentation

If you want to get a feeling for how the interface looks like and what kind of analysis you can do, check out our interactive documentation here.

You can run an analysis without any local installation on some provided demo data. We also provide a quick run-down for you to use the toll, so that you can get starte quickly. If you like what you see, you can install a local version as explained in this documentation and process your own data.

fq-interactive.png