Overview

ImJoy is image processing platform with an easy to use interface running in your browser.

  • While ImJoy is a browser app, NO user data will be transferred over the internet.
  • For best stability, we recommend using Chrome to run the ImJoy app.

  • Some of its main features are:

    1. Specific functionality is provided by plugins, which can be installed with simple links. Available plugins are listed in the plugin list on the left part of the interface. Plugins using Python require a Plugin engine to be executed. Installation and usasage is detailed below.

    2. ImJoy can have several workspaces. Each workspace can contain multiple plugins and is dedicated to a specific data processing task. Workspaces can be selected from little puzzle symbol in the upper left part of the interface.

imjoy-interface

Running Python plugins

Most of the provided plugins use Python for data processing. To use these plugins, you have to connect ImJoy to a Plugin engine. For this repository, we use Jupyter notebooks as and engine, which can be installed via Miniconda (see installation instructions).

Installing plugins

We provide links to install ImJoy plugins for the different workflows.

If you press on the installation link, the ImJoy app will open and display a dialog asking if you want to install the specified plugin. To confirm, press the install button.

imjoy-plugin-installation

These installation links also specify in which ImJoy workspaces the plugin will be installed.

Opening a workspace

Once a plugin is installed, ImJoy remembers the workspaces and plugins it contains.

If you want to redo an analysis, you simply have to open the ImJoy app and select the workspace fq-segmentation for this package.

If updates for the installed plugins are available, you will see a corresponding symbol next to the plugin name.

imjoy-workspacer.gif