ilastik-tasks

Collection of Fractal task to run Headless ilastik workflows.

Tasks

1. Pixel Classification Segmentation: A task to run a pixel classification workflow in headless mode. The task requires a trained ilastik project file and a list of input images. The task will run the pixel classification workflow on the input images, and label the connected components in the output image.

Installation and Deployment

• Install the mamba package manager

• Download the installation script from this repository

curl -O https://raw.githubusercontent.com/fractal-analytics-platform/fractal-ilastik-tasks/main/create_env_script.sh

• The scrip might require some small modifications.

VERSION="v0.1.1" # Version of the package to install (by default the latest version)
COMMMAND="mamba" # Command to use to create the environment (mamba or conda) 
# Location of the environment
# If ENVPREFIX is not NULL, the environment will be created with the prefix $ENVPREFIX/$ENVNAME 
# If ENVPREFIX is NULL, the environment will be created in the default location
ENVPREFIX="NULL" 

• Install the package using the installation script

bash create_env_script.sh

The installation script will create a conda environment with the name fractal-ilastik-tasks and install the package in the environment. It will also download the correct __FRACTAL_MANIFEST__.json file.

• In the fractal web interface add the task to the workflow as a "local env" task.