From 19fbcb92bfad0201e40a3e6493d8f5afa92a66d4 Mon Sep 17 00:00:00 2001
From: Sean <Sean.Donahue.5311@gmail.com>
Date: Mon, 1 Jun 2026 11:08:06 -0400
Subject: [PATCH 1/3] First pass at zarr ZipStore io support

---
 src/spatialdata/_io/_utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/spatialdata/_io/_utils.py b/src/spatialdata/_io/_utils.py
index 3be56d67..1c9ec287 100644
--- a/src/spatialdata/_io/_utils.py
+++ b/src/spatialdata/_io/_utils.py
@@ -23,7 +23,7 @@
 from upath import UPath
 from upath.implementations.local import PosixUPath, WindowsUPath
 from xarray import DataArray, DataTree
-from zarr.storage import FsspecStore, LocalStore
+from zarr.storage import FsspecStore, LocalStore, ZipStore
 
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
@@ -498,6 +498,9 @@ def _resolve_zarr_store(
         # if the input is a local path, use LocalStore
         return LocalStore(path.path)
 
+    if isinstance(path.store, ZipStore):
+        path = zarr.open_group(store=store, mode='r')
+
     if isinstance(path, zarr.Group):
         # if the input is a zarr.Group, wrap it with a store
         if isinstance(path.store, LocalStore):

From eb1ea7ea55bdfc6dd202d8eb13f10f2975aef37b Mon Sep 17 00:00:00 2001
From: pennycuda <141153875+pennycuda@users.noreply.github.com>
Date: Mon, 1 Jun 2026 14:44:01 -0400
Subject: [PATCH 2/3] allow zipped zarr files as inputs for read_zarr()

---
 src/spatialdata/_core/spatialdata.py |  5 +++-
 src/spatialdata/_io/_utils.py        | 12 ++++++++--
 src/spatialdata/_io/io_points.py     |  9 ++++++--
 src/spatialdata/_io/io_raster.py     | 15 ++++++++----
 src/spatialdata/_io/io_shapes.py     | 34 ++++++++++++++++++++++++----
 src/spatialdata/_io/io_table.py      | 16 +++++++++----
 src/spatialdata/_io/io_zarr.py       | 18 +++++++++++----
 7 files changed, 86 insertions(+), 23 deletions(-)

diff --git a/src/spatialdata/_core/spatialdata.py b/src/spatialdata/_core/spatialdata.py
index fb55ab08..396f10dc 100644
--- a/src/spatialdata/_core/spatialdata.py
+++ b/src/spatialdata/_core/spatialdata.py
@@ -7,6 +7,7 @@
 from collections.abc import Generator, Mapping
 from itertools import chain
 from pathlib import Path
+import shutil
 from typing import TYPE_CHECKING, Any, Literal
 
 import pandas as pd
@@ -1175,10 +1176,11 @@ def write(
 
         if isinstance(file_path, str):
             file_path = Path(file_path)
+
         self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
+        store = _resolve_zarr_store(file_path)
         self._validate_all_elements()
 
-        store = _resolve_zarr_store(file_path)
         zarr_format = parsed["SpatialData"].zarr_format
         zarr_group = zarr.create_group(store=store, overwrite=overwrite, zarr_format=zarr_format)
         self.write_attrs(zarr_group=zarr_group, sdata_format=parsed["SpatialData"])
@@ -1202,6 +1204,7 @@ def write(
         if consolidate_metadata:
             self.write_consolidated_metadata()
 
+
     def _write_element(
         self,
         element: SpatialElement | AnnData,
diff --git a/src/spatialdata/_io/_utils.py b/src/spatialdata/_io/_utils.py
index 1c9ec287..8822ba61 100644
--- a/src/spatialdata/_io/_utils.py
+++ b/src/spatialdata/_io/_utils.py
@@ -495,11 +495,17 @@ def _resolve_zarr_store(
         path = UPath(path)
 
     if isinstance(path, PosixUPath | WindowsUPath):
+        # if it is a zipped store, use ZipStore
+        if path.suffix == '.zip':
+            store = ZipStore(path.path)
+            store.root = path.path
+            return store
         # if the input is a local path, use LocalStore
         return LocalStore(path.path)
 
-    if isinstance(path.store, ZipStore):
-        path = zarr.open_group(store=store, mode='r')
+    if isinstance(path, ZipStore):
+        path.root =path.path
+        return path
 
     if isinstance(path, zarr.Group):
         # if the input is a zarr.Group, wrap it with a store
@@ -513,6 +519,8 @@ def _resolve_zarr_store(
         if isinstance(path.store, zarr.storage.ConsolidatedMetadataStore):
             # if the store is a ConsolidatedMetadataStore, just return the underlying FSSpec store
             return path.store.store
+        if isinstance(path.store, ZipStore):
+            return ZipStore(path.store)
         raise ValueError(f"Unsupported store type or zarr.Group: {type(path.store)}")
     if isinstance(path, zarr.storage.StoreLike):
         # if the input already a store, wrap it in an FSStore
diff --git a/src/spatialdata/_io/io_points.py b/src/spatialdata/_io/io_points.py
index 03ef3338..107da85f 100644
--- a/src/spatialdata/_io/io_points.py
+++ b/src/spatialdata/_io/io_points.py
@@ -6,6 +6,7 @@
 from dask.dataframe import DataFrame as DaskDataFrame
 from dask.dataframe import read_parquet
 from ome_zarr.format import Format
+from zarr.core.group import Group as ZarrGroup
 
 from spatialdata._io._utils import (
     _get_transformations_from_ngff_dict,
@@ -21,10 +22,14 @@
 
 
 def _read_points(
-    store: str | Path,
+    store: str | Path | ZarrGroup,
 ) -> DaskDataFrame:
     """Read points from a zarr store."""
-    f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
+    # fix for zipstore
+    if isinstance(store, ZarrGroup):
+        f = store
+    else:
+        f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
 
     version = _parse_version(f, expect_attrs_key=True)
     assert version is not None
diff --git a/src/spatialdata/_io/io_raster.py b/src/spatialdata/_io/io_raster.py
index 2feb7a77..018f481c 100644
--- a/src/spatialdata/_io/io_raster.py
+++ b/src/spatialdata/_io/io_raster.py
@@ -8,7 +8,7 @@
 import numpy as np
 import zarr
 from ome_zarr.format import Format
-from ome_zarr.io import ZarrLocation
+from ome_zarr.io import ZarrLocation, parse_url
 from ome_zarr.reader import Multiscales, Node, Reader
 from ome_zarr.types import JSONDict
 from ome_zarr.writer import _get_valid_axes
@@ -160,13 +160,18 @@ def _prepare_storage_options(
 
 
 def _read_multiscale(
-    store: str | Path, raster_type: Literal["image", "labels"], reader_format: Format
+    store: str | Path | zarr.storage.ZipStore, raster_type: Literal["image", "labels"], reader_format: Format
 ) -> DataArray | DataTree:
-    assert isinstance(store, str | Path)
+    assert isinstance(store, str | Path | zarr.storage.ZipStore | zarr.Group)
     assert raster_type in ["image", "labels"]
-
     nodes: list[Node] = []
-    image_loc = ZarrLocation(store, fmt=reader_format)
+    # instantiate an internal subpath for zipstores
+    internal_subpath = ""
+
+    image_loc = parse_url(store, fmt=reader_format)
+
+    if internal_subpath:
+        image_loc.internal_subpath = internal_subpath
     if exists := image_loc.exists():
         image_reader = Reader(image_loc)()
         image_nodes = list(image_reader)
diff --git a/src/spatialdata/_io/io_shapes.py b/src/spatialdata/_io/io_shapes.py
index 3b6e18e3..2c5669ab 100644
--- a/src/spatialdata/_io/io_shapes.py
+++ b/src/spatialdata/_io/io_shapes.py
@@ -9,6 +9,7 @@
 from natsort import natsorted
 from ome_zarr.format import Format
 from shapely import from_ragged_array, to_ragged_array
+from zarr.core.group import Group as ZarrGroup
 
 from spatialdata._io._utils import (
     _get_transformations_from_ngff_dict,
@@ -31,10 +32,14 @@
 
 
 def _read_shapes(
-    store: str | Path,
+    store: str | Path | ZarrGroup,
 ) -> GeoDataFrame:
     """Read shapes from a zarr store."""
-    f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
+    # fix for zipstore
+    if isinstance(store, ZarrGroup):
+        f = store
+    else:
+        f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
     version = _parse_version(f, expect_attrs_key=True)
     assert version is not None
     shape_format = ShapesFormats[version]
@@ -54,9 +59,28 @@ def _read_shapes(
             geometry = from_ragged_array(typ, coords, offsets)
             geo_df = GeoDataFrame({"geometry": geometry}, index=index)
     elif isinstance(shape_format, ShapesFormatV02 | ShapesFormatV03):
-        store_root = f.store_path.store.root
-        path = Path(store_root) / f.path / "shapes.parquet"
-        geo_df = read_parquet(path)
+        # fix for zipstores
+        if isinstance(f.store, zarr.storage.ZipStore):
+            import io
+
+            target_key = f"{f.path}/shapes.parquet" if f.path else "shapes.parquet"
+            target_key = target_key.strip('/')
+            if hasattr(f.store, "_zf") and f.store._zf is not None:
+                parquet_bytes = f.store._zf.read(target_key)
+            else:
+                from zarr.core.buffer import default_buffer_prototype
+                from zarr.core.sync import sync
+
+                buffer_obj = sync(f.store.get(target_key, prototype=default_buffer_prototype()))
+                parquet_bytes = buffer_obj.to_bytes() if buffer_obj else None
+            if parquet_bytes is None:
+                raise FileNotFoundError(f"Could not extract shapes.parquet inside zipped group path: {target_key}")
+            geo_df = read_parquet(io.BytesIO(parquet_bytes))
+        # original method
+        else:
+            store_root = f.store_path.store.root
+            path = Path(store_root) / f.path / "shapes.parquet"
+            geo_df = read_parquet(path)
     else:
         raise ValueError(
             f"Unsupported shapes format {shape_format} from version {version}. Please update the spatialdata library."
diff --git a/src/spatialdata/_io/io_table.py b/src/spatialdata/_io/io_table.py
index 3eb4b092..c9376eba 100644
--- a/src/spatialdata/_io/io_table.py
+++ b/src/spatialdata/_io/io_table.py
@@ -8,6 +8,7 @@
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.core.group import Group as ZarrGroup
 
 from spatialdata._io.format import (
     CurrentTablesFormat,
@@ -19,15 +20,22 @@
 from spatialdata.models import TableModel, get_table_keys
 
 
-def _read_table(store: str | Path) -> AnnData:
-    table = read_anndata_zarr(str(store))
+def _read_table(store: str | Path | ZarrGroup) -> AnnData:
+    # fix for zipstore
+    if isinstance(store, ZarrGroup):
+        f = store
+        table = read_anndata_zarr(f)
+    else:
+        table = read_anndata_zarr(str(store))
+        f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
 
-    f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
     version = _parse_version(f, expect_attrs_key=False)
     assert version is not None
     table_format = TablesFormats[version]
 
-    f.store.close()
+    # safely close non zipstores
+    if not isinstance(store, ZarrGroup):
+        f.store.close()
 
     if isinstance(table_format, TablesFormatV01 | TablesFormatV02):
         if TableModel.ATTRS_KEY in table.uns:
diff --git a/src/spatialdata/_io/io_zarr.py b/src/spatialdata/_io/io_zarr.py
index 4c410fab..a8cd4f67 100644
--- a/src/spatialdata/_io/io_zarr.py
+++ b/src/spatialdata/_io/io_zarr.py
@@ -32,7 +32,7 @@
 
 def _read_zarr_group_spatialdata_element(
     root_group: zarr.Group,
-    root_store_path: str,
+    root_store_path: str | zarr.storage.Store,
     sdata_version: Literal["0.1", "0.2"],
     selector: set[str],
     read_func: Callable[..., Any],
@@ -54,7 +54,12 @@ def _read_zarr_group_spatialdata_element(
                     # skip hidden files like .zgroup or .zmetadata
                     continue
                 elem_group = group[subgroup_name]
-                elem_group_path = os.path.join(root_store_path, elem_group.path)
+                # fix for zipstores
+                if isinstance(root_store_path, zarr.storage.ZipStore):
+                    elem_group_path = elem_group
+                # original functionality
+                else:
+                    elem_group_path = os.path.join(root_store_path, elem_group.path)
                 with handle_read_errors(
                     on_bad_files,
                     location=f"{group.path}/{subgroup_name}",
@@ -202,9 +207,10 @@ def read_zarr(
         element_type,
         element_container,
     ) in group_readers.items():
+        path_or_store = root_group.store if isinstance(root_group.store, zarr.storage.ZipStore) else root_store_path
         _read_zarr_group_spatialdata_element(
             root_group=root_group,
-            root_store_path=root_store_path,
+            root_store_path=path_or_store,
             sdata_version=sdata_version,
             selector=selector,
             read_func=read_func,
@@ -231,7 +237,11 @@ def read_zarr(
         tables=tables,
         attrs=attrs,
     )
-    sdata.path = resolved_store.root
+    # fix for zipstores
+    if isinstance(resolved_store.root, str):
+        sdata.path = Path(resolved_store.root)
+    else:
+        sdata.path = resolved_store.root
     return sdata
 
 

From b6f99829b0350b38697b4066ce4b946d3524ec75 Mon Sep 17 00:00:00 2001
From: pennycuda <141153875+pennycuda@users.noreply.github.com>
Date: Wed, 3 Jun 2026 16:37:44 -0400
Subject: [PATCH 3/3] run pre-commit

---
 src/spatialdata/_core/spatialdata.py | 2 --
 src/spatialdata/_io/_utils.py        | 4 ++--
 src/spatialdata/_io/io_points.py     | 7 +++----
 src/spatialdata/_io/io_raster.py     | 2 +-
 src/spatialdata/_io/io_shapes.py     | 9 ++++-----
 5 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/src/spatialdata/_core/spatialdata.py b/src/spatialdata/_core/spatialdata.py
index 396f10dc..5ca3065c 100644
--- a/src/spatialdata/_core/spatialdata.py
+++ b/src/spatialdata/_core/spatialdata.py
@@ -7,7 +7,6 @@
 from collections.abc import Generator, Mapping
 from itertools import chain
 from pathlib import Path
-import shutil
 from typing import TYPE_CHECKING, Any, Literal
 
 import pandas as pd
@@ -1204,7 +1203,6 @@ def write(
         if consolidate_metadata:
             self.write_consolidated_metadata()
 
-
     def _write_element(
         self,
         element: SpatialElement | AnnData,
diff --git a/src/spatialdata/_io/_utils.py b/src/spatialdata/_io/_utils.py
index 8822ba61..4cf9c938 100644
--- a/src/spatialdata/_io/_utils.py
+++ b/src/spatialdata/_io/_utils.py
@@ -496,7 +496,7 @@ def _resolve_zarr_store(
 
     if isinstance(path, PosixUPath | WindowsUPath):
         # if it is a zipped store, use ZipStore
-        if path.suffix == '.zip':
+        if path.suffix == ".zip":
             store = ZipStore(path.path)
             store.root = path.path
             return store
@@ -504,7 +504,7 @@ def _resolve_zarr_store(
         return LocalStore(path.path)
 
     if isinstance(path, ZipStore):
-        path.root =path.path
+        path.root = path.path
         return path
 
     if isinstance(path, zarr.Group):
diff --git a/src/spatialdata/_io/io_points.py b/src/spatialdata/_io/io_points.py
index 107da85f..c56ac41e 100644
--- a/src/spatialdata/_io/io_points.py
+++ b/src/spatialdata/_io/io_points.py
@@ -26,10 +26,9 @@ def _read_points(
 ) -> DaskDataFrame:
     """Read points from a zarr store."""
     # fix for zipstore
-    if isinstance(store, ZarrGroup):
-        f = store
-    else:
-        f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
+    f = (
+        store if isinstance(store, ZarrGroup) else zarr.open(Path(store), mode="r")
+    )  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
 
     version = _parse_version(f, expect_attrs_key=True)
     assert version is not None
diff --git a/src/spatialdata/_io/io_raster.py b/src/spatialdata/_io/io_raster.py
index 018f481c..15908d17 100644
--- a/src/spatialdata/_io/io_raster.py
+++ b/src/spatialdata/_io/io_raster.py
@@ -8,7 +8,7 @@
 import numpy as np
 import zarr
 from ome_zarr.format import Format
-from ome_zarr.io import ZarrLocation, parse_url
+from ome_zarr.io import parse_url
 from ome_zarr.reader import Multiscales, Node, Reader
 from ome_zarr.types import JSONDict
 from ome_zarr.writer import _get_valid_axes
diff --git a/src/spatialdata/_io/io_shapes.py b/src/spatialdata/_io/io_shapes.py
index 2c5669ab..73736c6d 100644
--- a/src/spatialdata/_io/io_shapes.py
+++ b/src/spatialdata/_io/io_shapes.py
@@ -36,10 +36,9 @@ def _read_shapes(
 ) -> GeoDataFrame:
     """Read shapes from a zarr store."""
     # fix for zipstore
-    if isinstance(store, ZarrGroup):
-        f = store
-    else:
-        f = zarr.open(Path(store), mode="r")  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
+    f = (
+        store if isinstance(store, ZarrGroup) else zarr.open(Path(store), mode="r")
+    )  # Path avoids zarr v3 URL-parsing special chars (e.g. #) in names
     version = _parse_version(f, expect_attrs_key=True)
     assert version is not None
     shape_format = ShapesFormats[version]
@@ -64,7 +63,7 @@ def _read_shapes(
             import io
 
             target_key = f"{f.path}/shapes.parquet" if f.path else "shapes.parquet"
-            target_key = target_key.strip('/')
+            target_key = target_key.strip("/")
             if hasattr(f.store, "_zf") and f.store._zf is not None:
                 parquet_bytes = f.store._zf.read(target_key)
             else: