Merge branch 'main' into dbit

quentinblampey · Feb 8, 2024 · b9ddfb0 · b9ddfb0
2 parents 90ba226 + 51202b6
commit b9ddfb0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning][].
 
 -   (MCMICRO) support for TMAs (such as the data of exemplar-002)
 -   (Xenium) support for post-xenium aligned images (IF, HE)
+-   (Xenium) reader for the selection coordinates file from the Xenium Explorer
 -   DBiT-seq reader
 
 ### Fixed

diff --git a/docs/api.md b/docs/api.md
@@ -8,6 +8,8 @@
 
 I/O for the `spatialdata` project.
 
+### Readers
+
 ```{eval-rst}
 .. autosummary::
     :toctree: generated
@@ -22,3 +24,13 @@ I/O for the `spatialdata` project.
     mcmicro
     dbit
 ```
+
+### Utility functions
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    xenium_aligned_image
+    xenium_explorer_selection
+```
diff --git a/docs/conf.py b/docs/conf.py
@@ -94,6 +94,7 @@
     "geopandas": ("https://geopandas.org/en/stable/", None),
     "xarray": ("https://docs.xarray.dev/en/stable/", None),
     "datatree": ("https://datatree.readthedocs.io/en/latest/", None),
+    "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
 }
 
 # List of patterns, relative to source directory, that match files and

diff --git a/src/spatialdata_io/__init__.py b/src/spatialdata_io/__init__.py
@@ -8,8 +8,24 @@
 from spatialdata_io.readers.merscope import merscope
 from spatialdata_io.readers.steinbock import steinbock
 from spatialdata_io.readers.visium import visium
-from spatialdata_io.readers.xenium import xenium
+from spatialdata_io.readers.xenium import (
+    xenium,
+    xenium_aligned_image,
+    xenium_explorer_selection,
+)
 
-__all__ = ["curio", "visium", "xenium", "codex", "cosmx", "mcmicro", "steinbock", "merscope", "dbit"]
+__all__ = [
+    "curio",
+    "visium",
+    "xenium",
+    "codex",
+    "cosmx",
+    "mcmicro",
+    "steinbock",
+    "merscope",
+    "xenium_aligned_image",
+    "xenium_explorer_selection",
+    "dbit"
+]
 
 __version__ = version("spatialdata-io")
diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py
@@ -28,7 +28,7 @@
 from spatialdata_io._utils import deprecation_alias
 from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
 
-__all__ = ["xenium"]
+__all__ = ["xenium", "xenium_aligned_image", "xenium_explorer_selection"]
 
 
 @deprecation_alias(cells_as_shapes="cells_as_circles")
@@ -325,3 +325,27 @@ def xenium_aligned_image(
         transformations={"global": transformation},
         **image_models_kwargs,
     )
+
+
+def xenium_explorer_selection(path: str | Path, pixel_size: float = 0.2125) -> Polygon:
+    """Read the coordinates of a selection `.csv` file exported from the `Xenium Explorer  <https://www.10xgenomics.com/support/software/xenium-explorer/latest>`_.
+
+    This file can be generated by the "Freehand Selection" or the "Rectangular Selection".
+    The output `Polygon` can be used for a polygon query on the pixel coordinate
+    system (by default, this is the `"global"` coordinate system for Xenium data).
+    If `spatialdata_xenium_explorer  <https://github.com/quentinblampey/spatialdata_xenium_explorer>`_ was used,
+    the `pixel_size` argument must be set to the one used during conversion with `spatialdata_xenium_explorer`.
+
+    Parameters
+    ----------
+    path
+        Path to the `.csv` file containing the selection coordinates
+    pixel_size
+        Size of a pixel in microns. By default, the Xenium pixel size is used.
+
+    Returns
+    -------
+    :class:`shapely.geometry.polygon.Polygon`
+    """
+    df = pd.read_csv(path, skiprows=2)
+    return Polygon(df.values / pixel_size)