add mcmicro

src/spatialdata_io/__init__.py

@@ -1,6 +1,7 @@
 from importlib.metadata import version
 
 from spatialdata_io.readers.cosmx import cosmx
+from spatialdata_io.readers.mcmicro import mcmicro
 from spatialdata_io.readers.steinbock import steinbock
 from spatialdata_io.readers.visium import visium
 from spatialdata_io.readers.xenium import xenium
@@ -9,6 +10,7 @@
     "visium",
     "xenium",
     "cosmx",
+    "mcmicro",
     "steinbock",
 ]
 

src/spatialdata_io/_constants/_constants.py

@@ -98,3 +98,22 @@ class SteinbockKeys(ModeEnum):
     # suffixes for images and labels
     IMAGE_SUFFIX = ".ome.tiff"
     LABEL_SUFFIX = ".tiff"
+
+
+@unique
+class McmicroKeys(ModeEnum):
+    """Keys for *Mcmicro* formatted dataset."""
+
+    # files and directories
+    CELL_FEATURES_SUFFIX = "--unmicst_cell.csv"
+    QUANTIFICATION_DIR = "quantification"
+    MARKERS_FILE = "markers.csv"
+    IMAGES_DIR = "registration"
+    IMAGE_SUFFIX = ".ome.tif"
+    LABELS_DIR = "segmentation"
+    LABELS_PREFIX = "unmicst-"
+
+    # metadata
+    COORDS_X = "X_centroid"
+    COORDS_Y = "Y_centroid"
+    INSTANCE_KEY = "CellID"

src/spatialdata_io/readers/mcmicro.py

@@ -0,0 +1,131 @@
+from __future__ import annotations
+
+import os
+from collections.abc import Mapping
+from pathlib import Path
+from types import MappingProxyType
+from typing import Any, Union
+
+import numpy as np
+import pandas as pd
+from anndata import AnnData
+from dask_image.imread import imread
+from multiscale_spatial_image.multiscale_spatial_image import MultiscaleSpatialImage
+from spatial_image import SpatialImage
+from spatialdata import Image2DModel, Labels2DModel, SpatialData, TableModel
+
+from spatialdata_io._constants._constants import McmicroKeys
+
+__all__ = ["mcmicro"]
+
+
+def _get_images(
+    path: Path,
+    sample: str,
+    imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
+    image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
+) -> Union[SpatialImage, MultiscaleSpatialImage]:
+    image = imread(path / McmicroKeys.IMAGES_DIR / f"{sample}{McmicroKeys.IMAGE_SUFFIX}", **imread_kwargs)
+    return Image2DModel.parse(image, **image_models_kwargs)
+
+
+def _get_labels(
+    path: Path,
+    sample: str,
+    labels_kind: str,
+    imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
+    image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
+) -> Union[SpatialImage, MultiscaleSpatialImage]:
+    image = imread(
+        path
+        / McmicroKeys.LABELS_DIR
+        / f"{McmicroKeys.LABELS_PREFIX}{sample}"
+        / f"{labels_kind}{McmicroKeys.IMAGE_SUFFIX}",
+        **imread_kwargs,
+    ).squeeze()
+    return Labels2DModel.parse(image, **image_models_kwargs)
+
+
+def _get_table(
+    path: Path,
+    sample: str,
+) -> AnnData:
+
+    table = pd.read_csv(path / McmicroKeys.QUANTIFICATION_DIR / f"{sample}{McmicroKeys.CELL_FEATURES_SUFFIX}")
+    markers = pd.read_csv(path / McmicroKeys.MARKERS_FILE)
+    markers.index = markers.marker_name
+    var = markers.marker_name.tolist()
+    coords = [McmicroKeys.COORDS_X, McmicroKeys.COORDS_Y]
+    adata = AnnData(
+        table[var].to_numpy(),
+        obs=table.drop(columns=var + coords),
+        var=markers,
+        obsm={"spatial": table[coords].to_numpy()},
+        dtype=np.float_,
+    )
+
+    return TableModel.parse(adata, region=sample, instance_key=McmicroKeys.INSTANCE_KEY)
+
+
+def mcmicro(
+    path: str | Path,
+    dataset_id: str,
+    imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
+    image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
+) -> SpatialData:
+    """
+    Read a *Mcmicro* output into a SpatialData object.
+
+    .. seealso::
+
+        - `Mcmicro pipeline  <https://mcmicro.org/>`_.
+
+    Parameters
+    ----------
+    path
+        Path to the dataset.
+    dataset_id
+        Dataset identifier.
+    imread_kwargs
+        Keyword arguments to pass to the image reader.
+    image_models_kwargs
+        Keyword arguments to pass to the image models.
+
+    Returns
+    -------
+    :class:`spatialdata.SpatialData`
+    """
+    path = Path(path)
+
+    samples = os.listdir(path / McmicroKeys.IMAGES_DIR)
+    if len(samples) > 1:
+        raise ValueError("Only one sample per dataset is supported.")
+    if (dataset_id + McmicroKeys.IMAGE_SUFFIX) not in samples:
+        raise ValueError("Dataset id is not consistent with sample name.")
+
+    images = {}
+    images[dataset_id] = _get_images(
+        path,
+        dataset_id,
+        imread_kwargs,
+        image_models_kwargs,
+    )
+    labels = {}
+    labels[dataset_id] = _get_labels(
+        path,
+        dataset_id,
+        "cell",
+        imread_kwargs,
+        image_models_kwargs,
+    )
+    labels[f"{dataset_id}_nuclei"] = _get_labels(
+        path,
+        dataset_id,
+        "nuclei",
+        imread_kwargs,
+        image_models_kwargs,
+    )
+
+    table = _get_table(path, dataset_id)
+
+    return SpatialData(images=images, labels=labels, table=table)