diff --git a/tools/anndata/import.xml b/tools/anndata/import.xml
index cc9466d2568..88d213cf305 100644
--- a/tools/anndata/import.xml
+++ b/tools/anndata/import.xml
@@ -14,7 +14,7 @@
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="1.10.2">scanpy</requirement>
+        <requirement type="package" version="1.10.4">scanpy</requirement>
     </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
diff --git a/tools/anndata/macros.xml b/tools/anndata/macros.xml
index 9f434e237b0..afdcc0e5964 100644
--- a/tools/anndata/macros.xml
+++ b/tools/anndata/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.10.9</token>
+    <token name="@TOOL_VERSION@">0.11.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
diff --git a/tools/anndata/modify_loom.xml b/tools/anndata/modify_loom.xml
index f89278e24de..1c2db5072af 100644
--- a/tools/anndata/modify_loom.xml
+++ b/tools/anndata/modify_loom.xml
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->
+        <requirement type="package" version="2.2.1">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->
     </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[