Merge pull request #75 from BioinfoTongLI/main

Added ISS support of Sanger data format

Author: LucaMarconato

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
 ### Added
 
 -   (Xenium) support reading multi-polygon selection files from the Xenium Explorer
+-   (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
 
 ### Fixed
 

docs/api.md

@@ -26,19 +26,26 @@ I/O for the `spatialdata` project.
     xenium
 ```
 
-### Conversion functions
-
-### Utility functions
+### Experimental readers
 
 ```{eval-rst}
+.. currentmodule:: spatialdata_io.experimental
+
 .. autosummary::
     :toctree: generated
 
-    xenium_aligned_image
-    xenium_explorer_selection
+    iss
 ```
 
-### Experimental readers
+### Conversion functions
+
+```{eval-rst}
+.. currentmodule:: spatialdata_io
+
+.. autosummary::
+    :toctree: generated
+
+```
 
 ### Experimental conversion functions
 
@@ -51,3 +58,15 @@ I/O for the `spatialdata` project.
     from_legacy_anndata
     to_legacy_anndata
 ```
+
+### Utility functions
+
+```{eval-rst}
+.. currentmodule:: spatialdata_io
+
+.. autosummary::
+    :toctree: generated
+
+    xenium_aligned_image
+    xenium_explorer_selection
+```

src/spatialdata_io/experimental/__init__.py

@@ -2,5 +2,6 @@
     from_legacy_anndata,
     to_legacy_anndata,
 )
+from spatialdata_io.readers.iss import iss
 
-__all__ = ["from_legacy_anndata", "to_legacy_anndata"]
+__all__ = ["from_legacy_anndata", "to_legacy_anndata", "iss"]

src/spatialdata_io/readers/iss.py

@@ -0,0 +1,109 @@
+from __future__ import annotations
+
+from collections.abc import Mapping
+from pathlib import Path
+from types import MappingProxyType
+from typing import Any
+
+import anndata as ad
+from dask_image.imread import imread
+from spatialdata import SpatialData
+from spatialdata.models import Image2DModel, Labels2DModel, TableModel
+from spatialdata.transformations.transformations import Identity
+from xarray import DataArray
+
+from spatialdata_io._docs import inject_docs
+
+__all__ = ["iss"]
+
+
+@inject_docs()
+def iss(
+    path: str | Path,
+    raw_relative_path: str | Path,
+    labels_relative_path: str | Path,
+    h5ad_relative_path: str | Path,
+    instance_key: str,
+    dataset_id: str = "region",
+    multiscale_image: bool = True,
+    multiscale_labels: bool = True,
+    imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
+    image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
+    labels_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
+) -> SpatialData:
+    """
+    Read *Sanger ISS* formatted dataset.
+
+    This function reads the following files:
+
+        - ``<dataset_id>``: Counts and metadata file.
+        - ``<raw_relative_path>``: Raw raster image.
+        - ``<labels_relative_path>``: Label image.
+
+    Parameters
+    ----------
+    path
+        Path to the directory containing the data.
+    raw_relative_path
+        Relative path to the raw raster image file.
+    labels_relative_path
+        Relative path to the label image file.
+    h5ad_relative_path
+        Relative path to the counts and metadata file.
+    instance_key
+        The name of the column that contains the instance identifiers.
+        Must be specified to link the table with the labels image (e.g. `cell_id`).
+    dataset_id
+        Dataset identifier.
+    multiscale_image
+        Whether to process the raw image into a multiscale image.
+    multiscale_labels
+        Whether to process the label image into a multiscale image.
+    imread_kwargs
+        Keyword arguments passed to :func:`dask_image.imread.imread`.
+    image_models_kwargs
+        Keyword arguments passed to :class:`spatialdata.models.Image2DModel`.
+    labels_models_kwargs
+        Keyword arguments passed to :class:`spatialdata.models.Labels2DModel`.
+
+    Returns
+    -------
+    The spatial data object containing the ISS data.
+    """
+    REGION = f"{dataset_id}_labels_image"
+    REGION_KEY = "region"
+    path = Path(path)
+
+    adata = ad.read(path / h5ad_relative_path)
+    adata.obs[instance_key] = adata.obs.index.astype(int)
+    adata.var_names_make_unique()
+    adata.obs[REGION_KEY] = REGION
+    table = TableModel.parse(adata, region=REGION, region_key=REGION_KEY, instance_key=instance_key)
+
+    transform_original = Identity()
+
+    labels_image = imread(path / labels_relative_path, **imread_kwargs).squeeze()
+    labels_image = DataArray(labels_image[2, :, :], dims=("y", "x"))
+
+    labels_image_parsed = Labels2DModel.parse(
+        labels_image,
+        scale_factors=[2, 2, 2, 2] if multiscale_labels else None,
+        transformations={"global": transform_original},
+        **labels_models_kwargs,
+    )
+
+    raw_image = imread(path / raw_relative_path, **imread_kwargs)
+    raw_image = DataArray(raw_image, dims=("c", "y", "x"))
+
+    raw_image_parsed = Image2DModel.parse(
+        raw_image,
+        scale_factors=[2, 2, 2, 2] if multiscale_image else None,
+        transformations={"global": transform_original},
+        **image_models_kwargs,
+    )
+
+    return SpatialData(
+        images={f"{dataset_id}_raw_image": raw_image_parsed},
+        labels={REGION: labels_image_parsed},
+        table=table,
+    )