opendvp.io.segmask_to_qupath

opendvp.io.segmask_to_qupath#

segmask_to_qupath(path_to_mask, simplify_value=1.0, save_as_detection=True)#

Convert a segmentation mask (TIFF) to QuPath-compatible detections as a GeoDataFrame or GeoJSON file.

This function loads a 2D segmentation mask image, converts it to polygons using spatialdata, and prepares the result for QuPath detection import. Optionally, it can simplify the geometry, export the detections as a GeoJSON file, and/or return the resulting GeoDataFrame.

Parameters:

  • path_to_mask (str or pathlib.Path) – Path to the segmentation mask image (must be a .tif file).

  • simplify_value (float, default 1) – Tolerance for geometry simplification. Set to None to disable simplification.

  • export_path (str, optional) – If provided, writes the detections to this path as a GeoJSON file.

  • return_gdf (bool, default False) – If True, returns the resulting GeoDataFrame. If False, returns None.

Returns:

The resulting GeoDataFrame if return_gdf is True, otherwise None.

Return type:

geopandas.GeoDataFrame or None

Raises:

  • ImportError – If required packages (dask, dask_image, spatialdata) are not installed.

  • ValueError – If input types or file extensions are incorrect.

Notes

  • Requires the ‘dask’, ‘dask_image’, and ‘spatialdata’ packages.

  • The exported GeoJSON is compatible with QuPath for detection import and visualization.

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