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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.
  • Images are exported in parallel — one Nextflow job per image.

Required parameters

  • --project Path to QuPath project (.qpproj).
  • --tile_width Tile width in pixels (for example 1024).
  • --tile_height Tile height 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_width 1024 \
	--tile_height 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.
  • logs/ directory containing one <image>_export.log per image.

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.