fractal-plantseg-tasks

Collection of Fractal task with the PlantSeg segmentation pipeline.

Tasks

1. Plantseg Workflow: The main PlantSeg segmentation pipeline. For detailed information on PlantSeg, please refer to the PlantSeg repository.
2. Tiff Converters: A Basic converter to convert a simple tiff file in OME-Zarr format.
3. HDF5 Converters: A Basic converter to convert a simple hdf5 file in OME-Zarr format.

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-plantseg-tasks/main/create_env_script.sh

• The scrip might require some small modifications.

VERSION="v0.1.0" # Version of the package to install (by default the latest version)
COMMMAND="mamba" # Command to use to create the environment (mamba or conda) 
CUDA="12.1" # Available options: 12.1, 11.8 or CPU (default is 12.1)
# 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-plantseg-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.
• Plantseg will download the necessary models on the first run. The default location for the models and data is ~/.plantseg_models. If your system has a very limited home directory, you can set the environment variable PLANTSEG_HOME to a different location.