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 [sections] how to use and install the Plugin engine to run these plugins.

Once a plugin is installed, it will be available for later use in the ImJoy workspace fq-segmentation as explained here.

Quick summary for how to connect ImJoy to Jupyter engine

  1. Open anaconda terminal.
  2. Activate environment: conda activate fq-segmentation
  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.

Typical workflows

For most purposes, the segmentation will consist of two steps. Each of these steps is described in a dedicated section. In this section you can also find a recommended workflow, which allows you to also process the test data.

  1. Pre-processing of the data: segmentation is performed on 2D images. If your images are 3D, you have to either split them, or project them into 2D images. This can be done with the pre-processing workflow.
  2. Actual segmentation of your images. We provide different plugins to segment. one type of structure, e.g. nuclei or cells, or two, e.g. cells and nuclei.

Each workflow is documented in a dedicated section. We provide

  • Installation links.
  • Detailed explanations of the different parameters.
  • A Recommended workflow for how to set the parameters following the recommended data organization.