diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1e54869b..5128f2f5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,18 +9,18 @@ ci:
     skip: []
 repos:
     - repo: https://github.com/rbubley/mirrors-prettier
-      rev: v3.5.3
+      rev: v3.7.4
       hooks:
           - id: prettier
             exclude: ^.github/workflows/test.yaml
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.15.0
+      rev: v1.19.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.11
+      rev: v0.14.10
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]
diff --git a/src/spatialdata/_core/query/relational_query.py b/src/spatialdata/_core/query/relational_query.py
index 247bffeb..3f0fa935 100644
--- a/src/spatialdata/_core/query/relational_query.py
+++ b/src/spatialdata/_core/query/relational_query.py
@@ -968,6 +968,7 @@ def get_values(
             assert obs[region_key].nunique() == 1
             assert obs[instance_key].nunique() == len(matched_table)
         else:
+            assert isinstance(element, AnnData)
             matched_table = element
             instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
             region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
diff --git a/src/spatialdata/_core/spatialdata.py b/src/spatialdata/_core/spatialdata.py
index 21bd6c5b..abc5e6ec 100644
--- a/src/spatialdata/_core/spatialdata.py
+++ b/src/spatialdata/_core/spatialdata.py
@@ -702,7 +702,7 @@ def _filter_tables(
 
                     assert element_names is not None
                     table = _filter_table_by_element_names(table, element_names)
-                    if len(table) != 0:
+                    if table is not None and len(table) != 0:
                         tables[table_name] = table
                 elif by == "elements":
                     from spatialdata._core.query.relational_query import (
@@ -711,7 +711,7 @@ def _filter_tables(
 
                     assert elements_dict is not None
                     table = _filter_table_by_elements(table, elements_dict=elements_dict)
-                    if len(table) != 0:
+                    if table is not None and len(table) != 0:
                         tables[table_name] = table
         else:
             tables = self.tables
diff --git a/src/spatialdata/_io/io_zarr.py b/src/spatialdata/_io/io_zarr.py
index 98919d61..0312dc96 100644
--- a/src/spatialdata/_io/io_zarr.py
+++ b/src/spatialdata/_io/io_zarr.py
@@ -158,7 +158,7 @@ def read_zarr(
     # the following is the SpatialDataContainerFormat version
     if "spatialdata_attrs" not in root_group.metadata.attributes:
         # backward compatibility for pre-versioned SpatialData zarr stores
-        sdata_version = cast(Literal["0.1", "0.2"], "0.1")
+        sdata_version: Literal["0.1", "0.2"] = "0.1"
     else:
         sdata_version = root_group.metadata.attributes["spatialdata_attrs"]["version"]
     if sdata_version == "0.1":