diff --git a/pyproject.toml b/pyproject.toml
index 94bae092..d0593234 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ dependencies = [
     "pyyaml",
     "ruffus",
     "scanorama",
-    "scanpy==1.9.6",
+    "scanpy==1.9.8",
     "leidenalg",
     "louvain",
     "scib",
@@ -62,6 +62,7 @@ spatial = [
     "jax==0.4.23",
     "jaxlib==0.4.23",
     "scvi-tools==1.0.4",
+    "scipy==1.12.0",
     "squidpy",
     "cell2location",
     "tangram-sc"