opendvp.io.adata_to_qupath#

opendvp.io.adata_to_qupath(adata, geodataframe, adataobs_on='CellID', gdf_on='CellID', gdf_index=False, classify_by=None, color_dict=None, simplify_value=1.0, save_as_detection=True)#

Export a GeoDataFrame with QuPath-compatible annotations, using AnnData for classification and color mapping.

This function matches shapes in a GeoDataFrame to metadata in an AnnData object. Assigns class labels and colors for QuPath visualization, and optionally simplifies geometries.

Parameters:#

adata: AnnData: AnnData object containing cell metadata (e.g., cell types, phenotypes).
geodataframe: GeoDataFrame: GeoDataFrame containing shapes (detections or annotations) to be exported.
adataobs_on: str, default “CellID”: Column in adata.obs to match with geodataframe.
gdf_on: str or None, default “CellID”: Column in geodataframe to match with adata.obs. If None and gdf_index is True, uses the index.
gdf_index: bool, default False: If True, uses the geodataframe index for matching instead of a column.
classify_by: str or None, optional: Column in adata.obs to use for classifying detections (e.g., cell type or phenotype).
color_dict: dict or None, optional: Dictionary mapping class/category names to RGB color lists (e.g., {‘Tcell’: [255, 0, 0]}). If not provided, a default color cycle will be generated. Hexcodes colors are acceptable as well.
simplify_value: float, default 1.0: Tolerance for geometry simplification. Set to None to disable simplification.
save_as_detection: bool, default True: If True, sets ‘objectType’ to ‘detection’ for QuPath.

returns:: The resulting GeoDataFrame with QuPath-compatible columns.
rtype:: GeoDataFrame
raises ValueError:: If input types are incorrect, required columns are missing, or no matches are found between adata and geodataframe.

Example

>>> import anndata as ad
>>> import geopandas as gpd
>>> from opendvp.io.adata_to_qupath import adata_to_qupath
>>> # Create example AnnData
>>> import pandas as pd
>>> obs = pd.DataFrame({'CellID': [1, 2, 3], 'celltype': ['A', 'B', 'A']})
>>> adata = ad.AnnData(obs=obs)
>>> # Create example GeoDataFrame
>>> from shapely.geometry import Point
>>> gdf = gpd.GeoDataFrame({'CellID': [1, 2, 3]}, geometry=[Point(0,0), Point(1,1), Point(2,2)])
>>> # Export with classification
>>> result = adata_to_qupath(
...     adata=adata,
...     geodataframe=gdf,
...     adataobs_on="CellID",
...     gdf_on="CellID",
...     classify_by="celltype",
...     color_dict={"A": [255,0,0], "B": [0,255,0]},
...     simplify_value=0.5,
...     save_as_detection=True
... )
>>> print(result.head())

opendvp.io.adata_to_qupath

Contents

opendvp.io.adata_to_qupath#

Parameters:#