In this folder you can find jupyter notebook examples to illustrate how to automate certain aspects of, and around ilastik from Python.
The structure in each folder will follow the same scheme:
notebooks/
├── subfolder # for a certain task
│ ├── task.ipynb # Notebook illustrating how to perform the task
│ └── environment.yml # conda environment definition needed to run the notebook
├── ...
We use conda for Python-based projects and recommend it for scientific Python development. It is assumed that you have already installed conda and are familiar with using a Terminal.
In order to run the notebook type the following in a Terminal/Command Line:
Note: conda has to be configured with strict channel priority in order to produce consistent environments.
# make sure to use strict channel priority - this setting is global but in general a good idea
conda config --set channel_priority strict
# create n environment - make sure to choose an appropriate <environment_name>
$ conda env create -n <environment_name> -f environment.yml
# this will produce a lot of output
$ conda activate <environment_name>
# start the notebook server in the current folder
$ jupyter notebook --notebook-dir .
# to close the server hit `ctrl + c` in the terminal shut down the server by confirming with `y`