Read ROIs from a QuPath GeoJSON file

Reads QuPath 0.4+ exports (a FeatureCollection or a bare feature array) and the legacy annotatR 0.1 dialect. classification.name (or the joined names of a derived class, e.g. "Tumor: Positive") becomes the ROI label, the classification colour the layer style colour, and features without a classification are labelled "unclassified". Everything else QuPath carries is kept, never invented, under each ROI's attributes$qupath: the object id and type, name, measurements (with explicit value_state), the image plane (zero-based c, z, t; c = NA for all channels), metadata, a nucleus geometry, and roi_native = "ellipse" with geometry_fidelity = "approximated" for polygonised ellipses. An annotatR id stored in metadata.annotatr_roi_id is restored as the ROI id.

Usage

at_read_qupath(
  path,
  layer_name = "qupath",
  level = 0L,
  call = rlang::caller_env()
)

Arguments

path

Path to a QuPath GeoJSON file.

layer_name

Layer name for the imported ROIs. Default "qupath".

level

Integer level to record on the ROIs. Default 0.

call

The calling environment, for error reporting.

Value

An annot_layer.

See also

Other io: at_load_project(), at_load_session(), at_read_geojson(), at_read_rois_csv(), at_roi_from_geojson(), at_save_project(), at_save_session(), at_write_geojson(), at_write_qupath(), at_write_rois_csv()