interactive learning and segmentation toolkit 1.4.0 quay.io/galaxy/ilastik:@VERSION@ 5800 1] #if len(duplicates) > 0: #set unique_duplicates = list(set(duplicates)) echo "Cannot run ilastik because these identifiers are present more than once:" && #for label in $unique_duplicates: echo $label && #end for exit 1 && #end if export HOME=\$PWD && ## Create a directory where the app user has access mkdir -p ./output && chown 1000:1000 ./output/ && ## Make a copy of the existing project if exists #if str($input_type.existing) == "existing": cp '$input_type.project' ./output/MyProject.ilp && #end if ## Link input images to current working directory #for input in $infiles: ln -s '$input' ./'$input.element_identifier'.tif && #end for ## Write the bash script to run: #if str($input_type.existing) == "new": echo "ilastik --new_project \$HOME/output/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args && #else: echo "ilastik --project \$HOME/output/MyProject.ilp" > ./ilastik_with_args && #end if ## Copy it to /bin/ so it will be used by the container: chmod +x ./ilastik_with_args && cp ./ilastik_with_args '/bin/' && /init ]]> Start a new project Modify an existing project Pixel Classification Autocontext (2-stage) Pixel Classification + Object Classification Object Classification [Inputs: Raw Data, Pixel Prediction Map] Object Classification [Inputs: Raw Data, Segmentation] Tracking [Inputs: Raw Data, Segmentation Image] Tracking [Inputs: Raw Data, Pixel Prediction Map] Animal Tracking [Inputs: Raw Data, Segmentation Image] Animal Tracking [Inputs: Raw Data, Pixel Prediction Map] Tracking with Learning [Inputs: Raw Data, Segmentation Image] Tracking with Learning [Inputs: Raw Data, Pixel Prediction Map] Bounary-based Segmentation with Multicut Cell Density Counting Data Conversion Neural Network Classification (Remote) Neural Network Classification (Local) 10.1038/s41592-019-0582-9