Install ilastik and OMERO Python bindings

In this section, we show how to install ilastik in a virtual environment. We will use the ilastik API to analyze data stored in an OMERO server. We will use OMERO.py to interact with the OMERO server.

Setup

We recommend to install the dependencies using Conda. In case you do not have a conda installation we recommend downloading and installing the latest version of Miniforge.

Create the environment running the commands below as written:

$ git clone https://github.com/ome/omero-guide-ilastik

$ cd omero-guide-ilastik

$ conda env create -f binder/environment.yml

and activate the newly created environment:

$ conda activate omero-guide-ilastik

Before creating a new environment, remember to deactivate the current one:

$ conda deactivate

See also Conda command reference.

The following steps are only required if you want to run the notebooks.

• If you installed Miniforge:

  • Open jupyter notebook i.e. jupyter notebook and select the omero-guide-ilastik kernel or [conda env:omero-guide-ilastik] according to what is available.

  To stop the notebook server, in the terminal where te server is running, press Ctrl C. The following question will be asked in the terminal Shutdown this notebook server (y/[n])?. Enter the desired choice.

• If you have an Anaconda installation:

  • Start Jupyter from the Anaconda-navigator

  • To register the environment, run python -m ipykernel install --user --name omero-guide-ilastik

  • Select the notebook you wish to run and select the Kernel>Change kernel>Python [conda env:omero-guide-ilastik] or Kernel>Change kernel>omero-guide-ilastik.