diff --git a/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml b/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml
index e349607..68e86d7 100644
--- a/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml
+++ b/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml
@@ -47,8 +47,8 @@ engines:
           - procps
       - type: python
         packages:
-          - spatialdata~=0.3.0
-          - spatialdata-io~=0.1.7
+          - spatialdata~=0.4.0
+          - spatialdata-io~=0.2.0
           - mudata~=0.3.1
     test_setup:
       - type: apt
diff --git a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
index 1a52c72..cf09481 100644
--- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -231,7 +231,7 @@ build_info:
   output: "target/executable/convert/from_cosmx_to_h5mu"
   executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
index 11c929d..021d0a6 100755
--- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
+++ b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu"
-LABEL org.opencontainers.image.created="2025-06-06T09:56:25Z"
+LABEL org.opencontainers.image.created="2025-06-11T09:39:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
diff --git a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
index db06fa4..3e1a002 100644
--- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -190,8 +190,8 @@ engines:
   - type: "python"
     user: false
     packages:
-    - "spatialdata~=0.3.0"
-    - "spatialdata-io~=0.1.7"
+    - "spatialdata~=0.4.0"
+    - "spatialdata-io~=0.2.0"
     - "mudata~=0.3.1"
     upgrade: true
   test_setup:
@@ -217,7 +217,7 @@ build_info:
   output: "target/executable/convert/from_spatialdata_to_h5mu"
   executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
index f074eb3..dd36247 100755
--- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
+++ b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
@@ -454,13 +454,13 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 RUN pip install --upgrade pip && \
-  pip install --upgrade --no-cache-dir "spatialdata~=0.3.0" "spatialdata-io~=0.1.7" "mudata~=0.3.1"
+  pip install --upgrade --no-cache-dir "spatialdata~=0.4.0" "spatialdata-io~=0.2.0" "mudata~=0.3.1"
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu"
-LABEL org.opencontainers.image.created="2025-06-06T09:56:25Z"
+LABEL org.opencontainers.image.created="2025-06-11T09:39:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
diff --git a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
index 2ae2c1b..8eba4bc 100644
--- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -314,7 +314,7 @@ build_info:
   output: "target/executable/convert/from_xenium_to_spatialdata"
   executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
index b297a33..fba84c4 100755
--- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
+++ b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata"
-LABEL org.opencontainers.image.created="2025-06-06T09:56:25Z"
+LABEL org.opencontainers.image.created="2025-06-11T09:39:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
diff --git a/target/executable/filter/subset_cosmx/.config.vsh.yaml b/target/executable/filter/subset_cosmx/.config.vsh.yaml
index 9e20432..48507f7 100644
--- a/target/executable/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/executable/filter/subset_cosmx/.config.vsh.yaml
@@ -217,7 +217,7 @@ build_info:
   output: "target/executable/filter/subset_cosmx"
   executable: "target/executable/filter/subset_cosmx/subset_cosmx"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/filter/subset_cosmx/subset_cosmx b/target/executable/filter/subset_cosmx/subset_cosmx
index a8c2cc2..e3753e5 100755
--- a/target/executable/filter/subset_cosmx/subset_cosmx
+++ b/target/executable/filter/subset_cosmx/subset_cosmx
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
-LABEL org.opencontainers.image.created="2025-06-06T09:56:25Z"
+LABEL org.opencontainers.image.created="2025-06-11T09:39:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
index c62861e..82de82a 100644
--- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -231,7 +231,7 @@ build_info:
   output: "target/nextflow/convert/from_cosmx_to_h5mu"
   executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
index ee43249..3848b0b 100644
--- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
@@ -3340,7 +3340,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
     "viash_version" : "0.9.3",
-    "git_commit" : "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4",
+    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
index 0ddfe3d..76651fb 100644
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -190,8 +190,8 @@ engines:
   - type: "python"
     user: false
     packages:
-    - "spatialdata~=0.3.0"
-    - "spatialdata-io~=0.1.7"
+    - "spatialdata~=0.4.0"
+    - "spatialdata-io~=0.2.0"
     - "mudata~=0.3.1"
     upgrade: true
   test_setup:
@@ -217,7 +217,7 @@ build_info:
   output: "target/nextflow/convert/from_spatialdata_to_h5mu"
   executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
index ab683e9..e1c2cdf 100644
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
@@ -3293,8 +3293,8 @@ meta = [
           "type" : "python",
           "user" : false,
           "packages" : [
-            "spatialdata~=0.3.0",
-            "spatialdata-io~=0.1.7",
+            "spatialdata~=0.4.0",
+            "spatialdata-io~=0.2.0",
             "mudata~=0.3.1"
           ],
           "upgrade" : true
@@ -3332,7 +3332,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
     "viash_version" : "0.9.3",
-    "git_commit" : "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4",
+    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
index d76352b..796a6aa 100644
--- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -314,7 +314,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_spatialdata"
   executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
index b914f09..1f559d6 100644
--- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
@@ -3430,7 +3430,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
     "viash_version" : "0.9.3",
-    "git_commit" : "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4",
+    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
index 42139a4..22c9dc4 100644
--- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
@@ -217,7 +217,7 @@ build_info:
   output: "target/nextflow/filter/subset_cosmx"
   executable: "target/nextflow/filter/subset_cosmx/main.nf"
   viash_version: "0.9.3"
-  git_commit: "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4"
+  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/filter/subset_cosmx/main.nf b/target/nextflow/filter/subset_cosmx/main.nf
index f35d67b..c2290bc 100644
--- a/target/nextflow/filter/subset_cosmx/main.nf
+++ b/target/nextflow/filter/subset_cosmx/main.nf
@@ -3322,7 +3322,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
     "viash_version" : "0.9.3",
-    "git_commit" : "f502b8c8edb0ca78b2f3f1eb43dcbcd966525fb4",
+    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {