diff --git a/pyproject.toml b/pyproject.toml
index 8180e13..d95bf9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ dependencies = [
   'pandas>=1.1.2',
   'black>=21.11b1',
   'numpy>=1.21.2',
-  'zarr>=2.5.0,<3',
+  'zarr>=3.0.0',
   'numcodecs>=0.5.7,<0.16.0',
 ]
 
@@ -65,7 +65,7 @@ all = [
   # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not
   # Reference: https://github.com/scverse/scanpy/pull/3115/files
   'scanpy>=1.10.2',
-  'ome-zarr<0.10.3',
+  'ome-zarr>=0.12.2',
   'tifffile>=2020.10.1',
 
   'jupyter-server-proxy>=1.5.2',
@@ -89,7 +89,7 @@ testing = []
 linting = []
 notebook = [
   'spatialdata>=0.3.0',
-  'dask[dataframe]==2024.11.1',
+  'dask[dataframe]>=2025.2.0',
   'marimo',
   'starlette>=0.42.0',
   'tqdm>=4.1.0',
@@ -115,7 +115,7 @@ dev = [
   'scikit-misc>=0.1.3',
   'autopep8>=2.0.2',
   'spatialdata>=0.3.0',
-  'dask[dataframe]==2024.11.1',
+  'dask[dataframe]>=2025.2.0',
 ]
 
 [tool.uv]