diff --git a/src/nichecompass/nichecompass/script.py b/src/nichecompass/nichecompass/script.py
index ec86f50..27e756b 100644
--- a/src/nichecompass/nichecompass/script.py
+++ b/src/nichecompass/nichecompass/script.py
@@ -4,7 +4,6 @@ import mudata as mu
 
 from nichecompass.models import NicheCompass
 from nichecompass.utils import add_gps_from_gp_dict_to_adata
-from torch.cuda import is_available as cuda_is_available
 
 ## VIASH START
 par = {
@@ -92,9 +91,6 @@ from setup_logger import setup_logger
 
 logger = setup_logger()
 
-use_gpu = cuda_is_available()
-logger.info("GPU enabled? %s", use_gpu)
-
 ## Read in data
 adata = mu.read_h5ad(par["input"], mod=par["modality"])
 
@@ -175,7 +171,7 @@ model = NicheCompass(
     n_addon_gp=par["n_addon_gp"],
     cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
     seed=par["random_state"],
-    use_cuda_if_available=use_gpu,
+    use_cuda_if_available=True,
 )
 
 logger.info("Training NicheCompass model...")
@@ -203,7 +199,7 @@ model.train(
     edge_batch_size=par["edge_batch_size"],
     node_batch_size=par["node_batch_size"],
     n_sampled_neighbors=par["n_sampled_neighbors"],
-    use_cuda_if_available=use_gpu,
+    use_cuda_if_available=True,
 )
 
 ## Save model and data
diff --git a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
index 3b2a63a..ee12e05 100644
--- a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
   output: "target/_private/executable/filter/subset_cosmx"
   executable: "target/_private/executable/filter/subset_cosmx/subset_cosmx"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/_private/executable/filter/subset_cosmx/subset_cosmx b/target/_private/executable/filter/subset_cosmx/subset_cosmx
index 5323550..88889d3 100755
--- a/target/_private/executable/filter/subset_cosmx/subset_cosmx
+++ b/target/_private/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="2026-01-21T10:40:04Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
index d9da37c..377b11c 100644
--- a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
   output: "target/_private/nextflow/filter/subset_cosmx"
   executable: "target/_private/nextflow/filter/subset_cosmx/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/_private/nextflow/filter/subset_cosmx/main.nf b/target/_private/nextflow/filter/subset_cosmx/main.nf
index a239e5a..e29d415 100644
--- a/target/_private/nextflow/filter/subset_cosmx/main.nf
+++ b/target/_private/nextflow/filter/subset_cosmx/main.nf
@@ -3334,7 +3334,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
index 51c86e2..f30b4f2 100644
--- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
@@ -154,7 +154,7 @@ build_info:
   output: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test"
   executable: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test
index d5f1a35..e0e60ca 100755
--- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test
+++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/niche nichecompass_leiden_test"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
index 06fd47f..744e230 100644
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
@@ -154,7 +154,7 @@ build_info:
   output: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test"
   executable: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf
index 8af899a..c2ac148 100644
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf
@@ -3234,7 +3234,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
index 933986c..de03cfe 100644
--- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -301,7 +301,7 @@ build_info:
   output: "target/executable/convert/from_cells2stats_to_h5mu"
   executable: "target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
index 5ae4f8e..e47f8dd 100755
--- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
+++ b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:04Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
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 9bacc1e..f0be718 100644
--- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
   output: "target/executable/convert/from_cosmx_to_h5mu"
   executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   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 6ccf01c..1195e1c 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
@@ -460,9 +460,9 @@ 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="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
index bd431e2..c70b4ee 100644
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -234,7 +234,7 @@ build_info:
   output: "target/executable/convert/from_cosmx_to_spatialexperiment"
   executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
index 1d2a0ef..43a1a10 100755
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:02Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:41Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
index 6aab665..6735bcf 100644
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
   output: "target/executable/convert/from_h5mu_to_spatialexperiment"
   executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
index f3c9464..e4d925d 100755
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
@@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:04Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 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 e73e16b..5633de9 100644
--- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -221,7 +221,7 @@ build_info:
   output: "target/executable/convert/from_spatialdata_to_h5mu"
   executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   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 932ee7c..3ee54ed 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
@@ -459,9 +459,9 @@ 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_spatialdata_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
index a5815ce..9d78700 100644
--- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -244,7 +244,7 @@ build_info:
   output: "target/executable/convert/from_xenium_to_h5mu"
   executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
index 3eca0de..1a6e179 100755
--- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
+++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 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 d07dc87..c930cab 100644
--- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -326,7 +326,7 @@ build_info:
   output: "target/executable/convert/from_xenium_to_spatialdata"
   executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   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 161961f..ec5649d 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
@@ -459,9 +459,9 @@ 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="2026-01-21T10:40:04Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
index caeb95d..a406bbd 100644
--- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
   output: "target/executable/convert/from_xenium_to_spatialexperiment"
   executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
index d8ab772..a1e9cd9 100755
--- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
@@ -462,9 +462,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
index 6453996..6ee0600 100644
--- a/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
+++ b/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
@@ -302,7 +302,7 @@ build_info:
   output: "target/executable/dataflow/concatenate_h5mu"
   executable: "target/executable/dataflow/concatenate_h5mu/concatenate_h5mu"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu b/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
index 059c506..0595c4c 100755
--- a/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
+++ b/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component dataflow concatenate_h5mu"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:04Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/mapping/spaceranger_count/.config.vsh.yaml b/target/executable/mapping/spaceranger_count/.config.vsh.yaml
index b5838d5..7277f9f 100644
--- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml
@@ -439,7 +439,7 @@ build_info:
   output: "target/executable/mapping/spaceranger_count"
   executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/mapping/spaceranger_count/spaceranger_count b/target/executable/mapping/spaceranger_count/spaceranger_count
index 1e3ae15..761437c 100755
--- a/target/executable/mapping/spaceranger_count/spaceranger_count
+++ b/target/executable/mapping/spaceranger_count/spaceranger_count
@@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml b/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
index e2509e2..1742ee6 100644
--- a/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
+++ b/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
@@ -269,7 +269,7 @@ build_info:
   output: "target/executable/neighbors/spatial_neighborhood_graph"
   executable: "target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph b/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
index 8fe0972..df78570 100755
--- a/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
+++ b/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component neighbors spatial_neighborhood_graph"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
diff --git a/target/executable/nichecompass/nichecompass/.config.vsh.yaml b/target/executable/nichecompass/nichecompass/.config.vsh.yaml
index c38646f..ad2769e 100644
--- a/target/executable/nichecompass/nichecompass/.config.vsh.yaml
+++ b/target/executable/nichecompass/nichecompass/.config.vsh.yaml
@@ -1003,7 +1003,7 @@ build_info:
   output: "target/executable/nichecompass/nichecompass"
   executable: "target/executable/nichecompass/nichecompass/nichecompass"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/executable/nichecompass/nichecompass/nichecompass b/target/executable/nichecompass/nichecompass/nichecompass
index 81f612a..bc33024 100755
--- a/target/executable/nichecompass/nichecompass/nichecompass
+++ b/target/executable/nichecompass/nichecompass/nichecompass
@@ -464,9 +464,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component nichecompass nichecompass"
-LABEL org.opencontainers.image.created="2026-01-21T10:40:02Z"
+LABEL org.opencontainers.image.created="2026-01-26T08:53:41Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
+LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER
@@ -3115,7 +3115,6 @@ import mudata as mu
 
 from nichecompass.models import NicheCompass
 from nichecompass.utils import add_gps_from_gp_dict_to_adata
-from torch.cuda import is_available as cuda_is_available
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3221,9 +3220,6 @@ from setup_logger import setup_logger
 
 logger = setup_logger()
 
-use_gpu = cuda_is_available()
-logger.info("GPU enabled? %s", use_gpu)
-
 ## Read in data
 adata = mu.read_h5ad(par["input"], mod=par["modality"])
 
@@ -3304,7 +3300,7 @@ model = NicheCompass(
     n_addon_gp=par["n_addon_gp"],
     cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
     seed=par["random_state"],
-    use_cuda_if_available=use_gpu,
+    use_cuda_if_available=True,
 )
 
 logger.info("Training NicheCompass model...")
@@ -3332,7 +3328,7 @@ model.train(
     edge_batch_size=par["edge_batch_size"],
     node_batch_size=par["node_batch_size"],
     n_sampled_neighbors=par["n_sampled_neighbors"],
-    use_cuda_if_available=use_gpu,
+    use_cuda_if_available=True,
 )
 
 ## Save model and data
diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
index d236deb..7d5bc9b 100644
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -301,7 +301,7 @@ build_info:
   output: "target/nextflow/convert/from_cells2stats_to_h5mu"
   executable: "target/nextflow/convert/from_cells2stats_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
index e271473..928da0f 100644
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
@@ -3399,7 +3399,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
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 10cf1ca..c12c5b9 100644
--- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
   output: "target/nextflow/convert/from_cosmx_to_h5mu"
   executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   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 d982b19..9fb8978 100644
--- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
@@ -3350,7 +3350,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
index 3f6bef2..17934ba 100644
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -234,7 +234,7 @@ build_info:
   output: "target/nextflow/convert/from_cosmx_to_spatialexperiment"
   executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
index 4f270cb..479cf3c 100644
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
@@ -3326,7 +3326,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
index c3f079f..fdf643c 100644
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
   output: "target/nextflow/convert/from_h5mu_to_spatialexperiment"
   executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
index c545f65..e07a2eb 100644
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
@@ -3332,7 +3332,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "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 9e52378..ce5489e 100644
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -221,7 +221,7 @@ build_info:
   output: "target/nextflow/convert/from_spatialdata_to_h5mu"
   executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   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 1624194..e9ae4b7 100644
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
@@ -3331,7 +3331,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
index 16614c9..aa40d4a 100644
--- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -244,7 +244,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_h5mu"
   executable: "target/nextflow/convert/from_xenium_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_xenium_to_h5mu/main.nf b/target/nextflow/convert/from_xenium_to_h5mu/main.nf
index 27c21c5..d1269df 100644
--- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf
@@ -3348,7 +3348,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "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 c097c20..4a36cb4 100644
--- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -326,7 +326,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_spatialdata"
   executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   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 5cd1a8c..d4f595c 100644
--- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
@@ -3443,7 +3443,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
index d7ad4bd..c550dfe 100644
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_spatialexperiment"
   executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
index 99183ea..3ed6c54 100644
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
@@ -3337,7 +3337,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
index 9d70f89..f41e2a3 100644
--- a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
+++ b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
@@ -302,7 +302,7 @@ build_info:
   output: "target/nextflow/dataflow/concatenate_h5mu"
   executable: "target/nextflow/dataflow/concatenate_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/dataflow/concatenate_h5mu/main.nf b/target/nextflow/dataflow/concatenate_h5mu/main.nf
index bdfc324..4780844 100644
--- a/target/nextflow/dataflow/concatenate_h5mu/main.nf
+++ b/target/nextflow/dataflow/concatenate_h5mu/main.nf
@@ -3399,7 +3399,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/concatenate_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
index 64ff268..5285377 100644
--- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
@@ -439,7 +439,7 @@ build_info:
   output: "target/nextflow/mapping/spaceranger_count"
   executable: "target/nextflow/mapping/spaceranger_count/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf
index 5fb4cdc..f9652c0 100644
--- a/target/nextflow/mapping/spaceranger_count/main.nf
+++ b/target/nextflow/mapping/spaceranger_count/main.nf
@@ -3569,7 +3569,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml b/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
index d9b98f1..b166100 100644
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
@@ -269,7 +269,7 @@ build_info:
   output: "target/nextflow/neighbors/spatial_neighborhood_graph"
   executable: "target/nextflow/neighbors/spatial_neighborhood_graph/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf b/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
index 1be1112..2a3e1c8 100644
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
@@ -3373,7 +3373,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/neighbors/spatial_neighborhood_graph",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml b/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml
index 638259d..0fe4078 100644
--- a/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml
+++ b/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml
@@ -1003,7 +1003,7 @@ build_info:
   output: "target/nextflow/nichecompass/nichecompass"
   executable: "target/nextflow/nichecompass/nichecompass/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
diff --git a/target/nextflow/nichecompass/nichecompass/main.nf b/target/nextflow/nichecompass/nichecompass/main.nf
index 98dcf83..4834a51 100644
--- a/target/nextflow/nichecompass/nichecompass/main.nf
+++ b/target/nextflow/nichecompass/nichecompass/main.nf
@@ -4138,7 +4138,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/nichecompass/nichecompass",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -4194,7 +4194,6 @@ import mudata as mu
 
 from nichecompass.models import NicheCompass
 from nichecompass.utils import add_gps_from_gp_dict_to_adata
-from torch.cuda import is_available as cuda_is_available
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -4300,9 +4299,6 @@ from setup_logger import setup_logger
 
 logger = setup_logger()
 
-use_gpu = cuda_is_available()
-logger.info("GPU enabled? %s", use_gpu)
-
 ## Read in data
 adata = mu.read_h5ad(par["input"], mod=par["modality"])
 
@@ -4383,7 +4379,7 @@ model = NicheCompass(
     n_addon_gp=par["n_addon_gp"],
     cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
     seed=par["random_state"],
-    use_cuda_if_available=use_gpu,
+    use_cuda_if_available=True,
 )
 
 logger.info("Training NicheCompass model...")
@@ -4411,7 +4407,7 @@ model.train(
     edge_batch_size=par["edge_batch_size"],
     node_batch_size=par["node_batch_size"],
     n_sampled_neighbors=par["n_sampled_neighbors"],
-    use_cuda_if_available=use_gpu,
+    use_cuda_if_available=True,
 )
 
 ## Save model and data
diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
index f539dac..6c2175e 100644
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
@@ -640,7 +640,7 @@ build_info:
   output: "target/nextflow/workflows/multiomics/spatial_process_samples"
   executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
   dependencies:
   - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"
diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
index 80d7a1d..2c61f9d 100644
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
@@ -3807,7 +3807,7 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml b/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml
index ab0b7f0..8ab1503 100644
--- a/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml
@@ -795,7 +795,7 @@ build_info:
   output: "target/nextflow/workflows/niche/nichecompass_leiden"
   executable: "target/nextflow/workflows/niche/nichecompass_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
   dependencies:
   - "target/nextflow/dataflow/concatenate_h5mu"
diff --git a/target/nextflow/workflows/niche/nichecompass_leiden/main.nf b/target/nextflow/workflows/niche/nichecompass_leiden/main.nf
index c46df2c..e330b73 100644
--- a/target/nextflow/workflows/niche/nichecompass_leiden/main.nf
+++ b/target/nextflow/workflows/niche/nichecompass_leiden/main.nf
@@ -3948,7 +3948,7 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/niche/nichecompass_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
index ac3af71..693c479 100644
--- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
+++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
@@ -387,7 +387,7 @@ build_info:
   output: "target/nextflow/workflows/qc/spatial_qc"
   executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
   viash_version: "0.9.4"
-  git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
+  git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
   dependencies:
   - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"
diff --git a/target/nextflow/workflows/qc/spatial_qc/main.nf b/target/nextflow/workflows/qc/spatial_qc/main.nf
index 8e6fba0..5792ed1 100644
--- a/target/nextflow/workflows/qc/spatial_qc/main.nf
+++ b/target/nextflow/workflows/qc/spatial_qc/main.nf
@@ -3505,7 +3505,7 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
     "viash_version" : "0.9.4",
-    "git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
+    "git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {