import_large_geojson

Nextflow pipeline for importing large GeoJSON cell annotations into a QuPath project using headless QuPath.

What it does

• Runs QuPath in CLI mode against a .qpproj project.
• Executes import_large_geojson.groovy to match and import GeoJSON files into each image in the project.
• Each GeoJSON file is matched to a project image by filename stem (e.g. image_001.geojson → image_001.ome.tif).
• Optionally clears existing objects before importing (default: yes).

Required parameters

• --project Path to QuPath project (.qpproj).
• --geojson_dir Directory containing GeoJSON files to import.

Optional parameters

• --qupath_bin Path to QuPath executable (default: /stornext/System/data/software/rhel/9/base/tools/QuPath/0.6.0/bin/QuPath).
• --script Groovy script path (default: bin/import_large_geojson.groovy).
• --clear_existing Clear all existing objects before importing (default: true).
• --file_pattern Pattern for matching GeoJSON files to images (default: {stem}.geojson). {stem} is replaced with the image name without extension.
• --outdir Output directory for log files (default: results).
• --publish_dir_mode Nextflow publishDir mode (default: copy).

Usage

nextflow run main.nf \
    --project /path/to/QuPath_project/project.qpproj \
    --geojson_dir /path/to/geojson_files/ \
    --outdir /path/to/output

With custom file pattern (e.g. for files named sample_segmentation.geojson):

nextflow run main.nf \
    --project /path/to/QuPath_project/project.qpproj \
    --geojson_dir /path/to/geojson_files/ \
    --file_pattern "{stem}_segmentation.geojson"

To keep existing objects (append mode):

nextflow run main.nf \
    --project /path/to/QuPath_project/project.qpproj \
    --geojson_dir /path/to/geojson_files/ \
    --clear_existing false

Resource profiles

Memory is the main resource for large GeoJSON imports. CPU count is low since QuPath imports are single-threaded.

Profile	Executor	Queue	CPUs	Memory	Time
standard (default)	slurm	regular	4	450 GB	48h
small	slurm	regular	4	128 GB	48h
medium	slurm	regular	4	480 GB	48h
large	slurm	regular	8	1200 GB	48h

Use -profile small, -profile medium, or -profile large to override.

Outputs

• qupath_geojson_import.log with full QuPath run logs including per-image import status.

Notes

• For large GeoJSON files (100GB+), use the medium or large profile to ensure enough memory.
• The Groovy script handles .ome.tif / .ome.tiff extensions when matching stems.
• Images with no matching GeoJSON file are skipped with a warning (not an error).