export_multiplex_image_tiles

Nextflow pipeline for exporting tiles from images in a QuPath project using QuPath headless mode and TileExporter.

What it does

• Runs QuPath from CLI in headless mode.
• Iterates through all images in a .qpproj project.
• Exports image tiles using user-defined tile size and overlap.
• Creates one folder per image containing that image's tile files.

Required parameters

• --project Path to QuPath project (.qpproj).
• --tile_size Tile size in pixels (for example 1024).
• --tile_overlap Tile overlap in pixels (for example 128).

Optional:

• --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/export_image_tiles.groovy). Relative paths are resolved from the pipeline directory.
• --downsample Downsample factor for tile export (default: 1.0).
• --include_partial_tiles Include edge tiles smaller than tile size (default: true).
• --outdir Output directory (default: results).

Usage

Run on HPC with Singularity and medium resources:

nextflow run main.nf \
	-profile singularity,medium \
	--project /path/to/project.qpproj \
	--qupath_bin /stornext/System/data/software/rhel/9/base/tools/QuPath/0.6.0/bin/QuPath \
	--tile_size 1024 \
	--tile_overlap 128 \
	--downsample 1.0 \
	--include_partial_tiles true \
	--outdir /path/to/output

Outputs

• tiles/ output directory containing one folder per image in the QuPath project.
• Per-image folder names are sanitized from QuPath image names.
• qupath_tile_export.log with the full QuPath export log.

Merging tile GeoJSON back to full-image GeoJSON

Use bin/merge_tile_geojson.py after segmentation on tiles.

Example:

python bin/merge_tile_geojson.py \
	--input-dir /path/to/tile_geojson \
	--output-dir /path/to/merged_geojson \
	--overlap 200 \
	--core-filter \
	--dedup-iou 0.4

Notes:

• The script parses tile offsets from filenames like [x=824,y=1648,w=1024,h=400].
• It shifts polygons into global coordinates before merging.
• --core-filter keeps objects whose centroid falls in the non-overlap core of each tile.
• --dedup-iou applies NMS-style duplicate removal in overlap regions.