From 51e076df8de28915fd25aa2ff32a7746d0e2a717 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Wed, 15 Oct 2025 17:31:50 +0200
Subject: [PATCH 01/12] update component for multimodal RDS

---
 _viash.yaml                                   |   3 +
 .../from_h5mu_to_seurat/config.vsh.yaml       |  65 ++++++++
 src/convert/from_h5mu_to_seurat/script.R      | 140 ++++++++++++++++++
 src/convert/from_h5mu_to_seurat/test.R        |  46 ++++++
 .../from_xenium_to_spatialexperiment/script.R |   6 +-
 5 files changed, 258 insertions(+), 2 deletions(-)
 create mode 100644 src/convert/from_h5mu_to_seurat/config.vsh.yaml
 create mode 100644 src/convert/from_h5mu_to_seurat/script.R
 create mode 100644 src/convert/from_h5mu_to_seurat/test.R

diff --git a/_viash.yaml b/_viash.yaml
index 504fcce..f64a065 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -21,6 +21,9 @@ info:
     - type: s3
       path: s3://openpipelines-bio/openpipeline_spatial/resources_test
       dest: resources_test
+    - type: s3
+      path: s3://openpipelines-data
+      dest: resources_test_sc
 
 config_mods: |
   .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
new file mode 100644
index 0000000..c8029aa
--- /dev/null
+++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
@@ -0,0 +1,65 @@
+name: "from_h5mu_to_seurat"
+namespace: "convert"
+scope: "public"
+description: |
+  Converts an h5ad file or a single modality of an h5mu file into a Seurat file.
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+arguments:
+  - name: "--input"
+    alternatives: ["-i"]
+    type: file
+    description: Input h5ad or h5mu file
+    direction: input
+    required: true
+    example: input.h5ad
+  - name: "--modality"
+    type: string
+    default: ["rna"]
+    multiple: true
+    example: ["rna", "prot", "vdj"]
+    required: false
+    description: Modality to be converted if the input file is an h5mu file.
+  - name: "--assay"
+    type: string
+    default: ["RNA"]
+    multiple: true
+    example: ["RNA", "ADT", "VDJ"]
+    description: |
+      Name of the assay to be created.
+      Order should match the order of the --modalities.
+      If layer dimensions of a modality are 0, the modality will be moved to the metadata instead of an assay.
+  - name: "--output"
+    alternatives: ["-o"]
+    type: file
+    description: Output Seurat file
+    direction: output
+    required: true
+    example: output.rds
+resources:
+  - type: r_script
+    path: script.R
+test_resources:
+  - type: r_script
+    path: test.R
+  - path: /resources_test_sc/pbmc_1k_protein_v3/
+  - path: /resources_test_sc/10x_5k_anticmv/
+engines:
+  - type: docker
+    image: rocker/r2u:22.04
+    setup:
+      - type: apt
+        packages: [ libhdf5-dev, libgeos-dev, hdf5-tools ]
+      - type: r
+        cran: [ anndata, hdf5r, Seurat, SeuratObject ]
+        github: scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a
+        bioc: [ rhdf5]
+    test_setup:
+      - type: r
+        cran: [ testthat ]
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [lowmem, singlecpu]
diff --git a/src/convert/from_h5mu_to_seurat/script.R b/src/convert/from_h5mu_to_seurat/script.R
new file mode 100644
index 0000000..2b4dd67
--- /dev/null
+++ b/src/convert/from_h5mu_to_seurat/script.R
@@ -0,0 +1,140 @@
+library(anndataR)
+library(hdf5r)
+# library(Seurat)
+
+### VIASH START
+par <- list(
+  input = "resources_test_sc/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect.h5mu",
+  output = "resources_test_sc/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect.rds",
+  assay = c("RNA", "ADT", "TCR"),
+  modality = c("rna", "prot", "vdj_t")
+)
+### VIASH END
+
+h5mu_to_h5ad <- function(h5mu_path, modality_name) {
+  tmp_path <- tempfile(fileext = ".h5ad")
+  mod_location <- paste("mod", modality_name, sep = "/")
+  h5src <- hdf5r::H5File$new(h5mu_path, "r")
+  h5dest <- hdf5r::H5File$new(tmp_path, "w")
+  # Copy over the child objects and the child attributes from root
+  # Root cannot be copied directly because it always exists and
+  # copying does not allow overwriting.
+  children <- hdf5r::list.objects(h5src,
+    path = mod_location,
+    full.names = FALSE, recursive = FALSE
+  )
+  for (child in children) {
+    h5dest$obj_copy_from(
+      h5src, paste(mod_location, child, sep = "/"),
+      paste0("/", child)
+    )
+  }
+  # Also copy the root attributes
+  root_attrs <- hdf5r::h5attr_names(x = h5src)
+  for (attr in root_attrs) {
+    h5a <- h5src$attr_open(attr_name = attr)
+    robj <- h5a$read()
+    h5dest$create_attr_by_name(
+      attr_name = attr,
+      obj_name = ".",
+      robj = robj,
+      space = h5a$get_space(),
+      dtype = h5a$get_type()
+    )
+  }
+  h5src$close()
+  h5dest$close()
+
+  tmp_path
+}
+
+has_zero_dimension <- function(adata) {
+  adata_dims <- adata$shape()
+  any(adata_dims == 0)
+}
+
+map_obs_to_metadata <- function(adata, seurat_obj, mod, assay) {
+  cells <- colnames(seurat_obj)
+  mod_meta <- adata$obs
+  obs_names <- rownames(mod_meta)
+  colnames(mod_meta) <- paste0(assay, "_", make.names(colnames(mod_meta)))
+
+  if (!all(obs_names %in% cells)) {
+    stop(paste0(
+      "Not all cells in the adata modality", mod,
+      "are present in the Seurat object."
+    )
+    )
+  }
+  mod_meta <- mod_meta[match(cells, obs_names), , drop = FALSE]
+  rownames(mod_meta) <- cells
+
+  seurat_obj <- AddMetaData(seurat_obj, mod_meta)
+}
+
+map_modality_to_assay <- function(adata, seurat_obj, mod, assay) {
+
+
+}
+
+# Initialize seurat object
+seurat_obj <- NULL
+modalities_to_metadata <- list()
+
+# Check that modalities and assays have the same length
+if (length(par$modality) != length(par$assay)) {
+  stop("The number of modalities should match the number of assays.")
+}
+
+# Loop through modalities and assays
+for (i in seq_along(par$modality)) {
+  cat("Processing modality:", par$modality[i], "as assay:", par$assay[i], "\n")
+
+  # Read the specific modality from h5mu file
+  adata_path <- h5mu_to_h5ad(par$input, par$modality[i])
+  adata <- read_h5ad(adata_path, mode = "r+")
+
+  # Check dimensions
+  # Modalities with dimension 0 will be added later
+  if (has_zero_dimension(adata)) {
+    if (adata$shape()[1] == 0) {
+      cat("Skipping modality", par$modality[i], "- has zero observations\n")
+    } else {
+      cat(
+        "Modality",
+        par$modality[i],
+        "has zero features - moving to metadata\n"
+      )
+      modalities_to_metadata[[par$modality[i]]] <- par$assay[i]
+    }
+    next
+  }
+
+  # Convert to Seurat assay
+  temp_seurat <- read_h5ad(
+    adata_path,
+    mode = "r",
+    as = "Seurat",
+    assay_name = par$assay[i]
+  )
+
+  # If this is the first modality, initialize the main Seurat object
+  if (is.null(seurat_obj)) {
+    seurat_obj <- temp_seurat
+  } else {
+    # Add as additional assay to existing Seurat object
+    seurat_obj[[par$assay[i]]] <- temp_seurat[[par$assay[i]]]
+  }
+}
+
+if (is.null(seurat_obj)) {
+  stop("No valid modalities found to create a Seurat object. At least one modality must have non-zero dimensions.")
+}
+
+for (mod in names(modalities_to_metadata)) {
+  assay <- modalities_to_metadata[[mod]]
+  cat("Moving modality", mod, "to metadata\n")
+  seurat_obj <- map_obs_to_metadata(adata, seurat_obj, mod, assay)
+}
+
+saveRDS(seurat_obj, file = par$output)
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
new file mode 100644
index 0000000..95aa302
--- /dev/null
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -0,0 +1,46 @@
+library(testthat, warn.conflicts = FALSE)
+library(hdf5r)
+
+
+## VIASH START
+meta <- list(
+  executable = "target/executable/convert/from_h5ad_to_seurat",
+  resources_dir = "resources_test",
+  name = "from_h5ad_to_seurat"
+)
+## VIASH END
+
+cat("> Checking conversion of h5mu file\n")
+
+in_h5mu <- paste0(
+  meta[["resources_dir"]],
+  "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
+)
+out_rds <- "output.rds"
+
+cat("> Running ", meta[["name"]], "\n", sep = "")
+out <- processx::run(
+  meta[["executable"]],
+  c(
+    "--input", in_h5mu,
+    "--output", out_rds
+  )
+)
+
+cat("> Checking whether output file exists\n")
+expect_equal(out$status, 0)
+expect_true(file.exists(out_rds))
+
+cat("> Reading output file\n")
+obj <- readRDS(file = out_rds)
+
+cat("> Checking whether Seurat object is in the right format\n")
+expect_is(obj, "Seurat")
+expect_equal(names(slot(obj, "assays")), "RNA")
+
+dim_rds <- dim(obj)
+mu_in <- H5File$new(in_h5mu, mode = "r")
+dim_ad <- mu_in[["/mod/rna/X"]]$attr_open("shape")$read()
+
+expect_equal(dim_rds[1], dim_ad[2])
+expect_equal(dim_rds[2], dim_ad[1])
diff --git a/src/convert/from_xenium_to_spatialexperiment/script.R b/src/convert/from_xenium_to_spatialexperiment/script.R
index 16cf22f..5c46b1f 100644
--- a/src/convert/from_xenium_to_spatialexperiment/script.R
+++ b/src/convert/from_xenium_to_spatialexperiment/script.R
@@ -2,7 +2,7 @@ library(SpatialExperimentIO)
 
 ### VIASH START
 par <- list(
-  input = "resources_test/xenium/temp_dir.zip",
+  input = "output-XETG00150__0031015__slidearray0085__20241023__195946",
   add_experiment_xenium = TRUE,
   add_parquet_paths = TRUE,
   alternative_experiment_features = c(
@@ -46,7 +46,9 @@ spe <- readXeniumSXE(
   coordNames = c("x_centroid", "y_centroid"),
   addExperimentXenium = par$add_experiment_xenium,
   addParquetPaths = par$add_parquet_paths,
-  altExps = par$alternative_experiment_features
+  altExps = par$alternative_experiment_features,
+  addCellBound = TRUE,
+  addNucBound = TRUE
 )
 
 cat("Saving output...")

From fceb33fa3324ba08b3fc61f301eb4cfd5734da23 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Wed, 15 Oct 2025 17:32:31 +0200
Subject: [PATCH 02/12] update gitingnore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 97dc208..606d4b8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,6 +25,7 @@ out/
 output*
 output_log/
 resources_test
+resources_test_sc
 /viash_tools/
 /test/
 

From 8eefdf9c526b11195a14bb052485b3d33bb2f7a2 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Wed, 15 Oct 2025 18:00:59 +0200
Subject: [PATCH 03/12] expand tests

---
 .../from_h5mu_to_seurat/config.vsh.yaml       |  2 +-
 src/convert/from_h5mu_to_seurat/script.R      | 51 +++++++-------
 src/convert/from_h5mu_to_seurat/test.R        | 70 ++++++++++++++++++-
 3 files changed, 95 insertions(+), 28 deletions(-)

diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
index c8029aa..0b9f59b 100644
--- a/src/convert/from_h5mu_to_seurat/config.vsh.yaml
+++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
@@ -52,7 +52,7 @@ engines:
       - type: apt
         packages: [ libhdf5-dev, libgeos-dev, hdf5-tools ]
       - type: r
-        cran: [ anndata, hdf5r, Seurat, SeuratObject ]
+        cran: [ anndata, hdf5r, Matrix, SeuratObject, Seurat ]
         github: scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a
         bioc: [ rhdf5]
     test_setup:
diff --git a/src/convert/from_h5mu_to_seurat/script.R b/src/convert/from_h5mu_to_seurat/script.R
index 2b4dd67..093b530 100644
--- a/src/convert/from_h5mu_to_seurat/script.R
+++ b/src/convert/from_h5mu_to_seurat/script.R
@@ -1,6 +1,6 @@
 library(anndataR)
 library(hdf5r)
-# library(Seurat)
+library(Seurat)
 
 ### VIASH START
 par <- list(
@@ -72,9 +72,22 @@ map_obs_to_metadata <- function(adata, seurat_obj, mod, assay) {
   seurat_obj <- AddMetaData(seurat_obj, mod_meta)
 }
 
-map_modality_to_assay <- function(adata, seurat_obj, mod, assay) {
-
+map_modality_to_assay <- function(adata, seurat_obj, assay) {
+  temp_seurat <- read_h5ad(
+    adata,
+    mode = "r",
+    as = "Seurat",
+    assay_name = assay
+  )
 
+  # If this is the first modality, initialize the main Seurat object
+  if (is.null(seurat_obj)) {
+    seurat_obj <- temp_seurat
+  } else {
+    # Add as additional assay to existing Seurat object
+    seurat_obj[[assay]] <- temp_seurat[[assay]]
+  }
+  seurat_obj
 }
 
 # Initialize seurat object
@@ -88,43 +101,31 @@ if (length(par$modality) != length(par$assay)) {
 
 # Loop through modalities and assays
 for (i in seq_along(par$modality)) {
-  cat("Processing modality:", par$modality[i], "as assay:", par$assay[i], "\n")
+  mod <- par$modality[i]
+  assay <- par$assay[i]
+  cat("Processing modality:", mod, "as assay:", assay, "\n")
 
   # Read the specific modality from h5mu file
-  adata_path <- h5mu_to_h5ad(par$input, par$modality[i])
-  adata <- read_h5ad(adata_path, mode = "r+")
+  adata_path <- h5mu_to_h5ad(par$input, mod)
+  adata <- read_h5ad(adata_path, mode = "r")
 
-  # Check dimensions
-  # Modalities with dimension 0 will be added later
+  # Check dimensions: modalities with dimension 0 will be added later
   if (has_zero_dimension(adata)) {
     if (adata$shape()[1] == 0) {
-      cat("Skipping modality", par$modality[i], "- has zero observations\n")
+      cat("Skipping modality", mod, "- has zero observations\n")
     } else {
       cat(
         "Modality",
-        par$modality[i],
+        mod,
         "has zero features - moving to metadata\n"
       )
-      modalities_to_metadata[[par$modality[i]]] <- par$assay[i]
+      modalities_to_metadata[[mod]] <- assay
     }
     next
   }
 
   # Convert to Seurat assay
-  temp_seurat <- read_h5ad(
-    adata_path,
-    mode = "r",
-    as = "Seurat",
-    assay_name = par$assay[i]
-  )
-
-  # If this is the first modality, initialize the main Seurat object
-  if (is.null(seurat_obj)) {
-    seurat_obj <- temp_seurat
-  } else {
-    # Add as additional assay to existing Seurat object
-    seurat_obj[[par$assay[i]]] <- temp_seurat[[par$assay[i]]]
-  }
+  seurat_obj <- map_modality_to_assay(adata_path, seurat_obj, assay)
 }
 
 if (is.null(seurat_obj)) {
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index 95aa302..4f38dc1 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -5,12 +5,13 @@ library(hdf5r)
 ## VIASH START
 meta <- list(
   executable = "target/executable/convert/from_h5ad_to_seurat",
-  resources_dir = "resources_test",
+  resources_dir = "resources_test_sc",
   name = "from_h5ad_to_seurat"
 )
 ## VIASH END
 
-cat("> Checking conversion of h5mu file\n")
+## Simple conversion
+cat("> Checking conversion of single-modality of h5mu file\n")
 
 in_h5mu <- paste0(
   meta[["resources_dir"]],
@@ -44,3 +45,68 @@ dim_ad <- mu_in[["/mod/rna/X"]]$attr_open("shape")$read()
 
 expect_equal(dim_rds[1], dim_ad[2])
 expect_equal(dim_rds[2], dim_ad[1])
+
+## Multi-modal conversion
+cat("> Checking conversion of multi-modal h5mu file\n")
+
+in_h5mu <- paste0(
+  meta[["resources_dir"]],
+  "/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect.h5mu"
+)
+out_rds <- "output.rds"
+
+cat("> Running ", meta[["name"]], "\n", sep = "")
+out <- processx::run(
+  meta[["executable"]],
+  c(
+    "--input", in_h5mu,
+    "--modality", "rna",
+    "--modality", "prot",
+    "--modality", "vdj_t",
+    "--assay", "RNA",
+    "--assay", "ADT",
+    "--assay", "TCR",
+    "--output", out_rds
+  )
+)
+
+cat("> Checking whether output file exists\n")
+expect_equal(out$status, 0)
+expect_true(file.exists(out_rds))
+
+cat("> Reading output file\n")
+obj <- readRDS(file = out_rds)
+
+cat("> Checking whether Seurat object is in the right format\n")
+expect_is(obj, "Seurat")
+expect_true(all(names(slot(obj, "assays")) %in% c("RNA", "ADT")))
+
+dim_rds <- dim(obj)
+mu_in <- H5File$new(in_h5mu, mode = "r")
+dim_ad <- mu_in[["/mod/rna/X"]]$attr_open("shape")$read()
+
+expect_equal(dim_rds[1], dim_ad[2])
+expect_equal(dim_rds[2], dim_ad[1])
+
+vdj_t_cols <- c(
+  "TCR_is_cell", "TCR_high_confidence", "TCR_multi_chain", "TCR_extra_chains",
+  "TCR_IR_VJ_1_c_call", "TCR_IR_VJ_2_c_call", "TCR_IR_VDJ_1_c_call",
+  "TCR_IR_VDJ_2_c_call", "TCR_IR_VJ_1_consensus_count",
+  "TCR_IR_VJ_2_consensus_count", "TCR_IR_VDJ_1_consensus_count",
+  "TCR_IR_VDJ_2_consensus_count", "TCR_IR_VJ_1_d_call",
+  "TCR_IR_VJ_2_d_call", "TCR_IR_VDJ_1_d_call", "TCR_IR_VDJ_2_d_call",
+  "TCR_IR_VJ_1_duplicate_count", "TCR_IR_VJ_2_duplicate_count",
+  "TCR_IR_VDJ_1_duplicate_count", "TCR_IR_VDJ_2_duplicate_count",
+  "TCR_IR_VJ_1_j_call", "TCR_IR_VJ_2_j_call", "TCR_IR_VDJ_1_j_call",
+  "TCR_IR_VDJ_2_j_call", "TCR_IR_VJ_1_junction", "TCR_IR_VJ_2_junction",
+  "TCR_IR_VDJ_1_junction", "TCR_IR_VDJ_2_junction", "TCR_IR_VJ_1_junction_aa",
+  "TCR_IR_VJ_2_junction_aa", "TCR_IR_VDJ_1_junction_aa", "TCR_IR_VDJ_2_junction_aa",
+  "TCR_IR_VJ_1_locus", "TCR_IR_VJ_2_locus", "TCR_IR_VDJ_1_locus",
+  "TCR_IR_VDJ_2_locus", "TCR_IR_VJ_1_productive", "TCR_IR_VJ_2_productive",
+  "TCR_IR_VDJ_1_productive", "TCR_IR_VDJ_2_productive", "TCR_IR_VJ_1_v_call",
+  "TCR_IR_VJ_2_v_call", "TCR_IR_VDJ_1_v_call", "TCR_IR_VDJ_2_v_call", "TCR_has_ir"
+)
+obs_cols <- c("orig.ident", "nCount_RNA", "nFeature_RNA")
+
+expect_true(all(vdj_t_cols %in% colnames(obj@meta.data)))
+expect_true(all(obs_cols %in% colnames(obj@meta.data)))
\ No newline at end of file

From 7c6e0b3932a615d8aa4bf0c7c67b934aa6ffd1c2 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Wed, 15 Oct 2025 18:09:16 +0200
Subject: [PATCH 04/12] lint

---
 src/convert/from_cosmx_to_spatialexperiment/test.R | 5 +++--
 src/convert/from_h5mu_to_seurat/script.R           | 3 +--
 src/convert/from_h5mu_to_seurat/test.R             | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/convert/from_cosmx_to_spatialexperiment/test.R b/src/convert/from_cosmx_to_spatialexperiment/test.R
index 3424487..771035b 100644
--- a/src/convert/from_cosmx_to_spatialexperiment/test.R
+++ b/src/convert/from_cosmx_to_spatialexperiment/test.R
@@ -75,8 +75,9 @@ spe <- paste0(meta[["resources_dir"]], "/Lung5_Rep2_tiny")
 out_rds <- "output.rds"
 
 create_folder_archive <- function(
-    folder_path,
-    archive = "Lung5_Rep2_tiny.zip") {
+  folder_path,
+  archive = "Lung5_Rep2_tiny.zip"
+) {
   old_wd <- getwd()
   on.exit(setwd(old_wd))
   setwd(meta$resources_dir)
diff --git a/src/convert/from_h5mu_to_seurat/script.R b/src/convert/from_h5mu_to_seurat/script.R
index 093b530..0c780e3 100644
--- a/src/convert/from_h5mu_to_seurat/script.R
+++ b/src/convert/from_h5mu_to_seurat/script.R
@@ -63,8 +63,7 @@ map_obs_to_metadata <- function(adata, seurat_obj, mod, assay) {
     stop(paste0(
       "Not all cells in the adata modality", mod,
       "are present in the Seurat object."
-    )
-    )
+    ))
   }
   mod_meta <- mod_meta[match(cells, obs_names), , drop = FALSE]
   rownames(mod_meta) <- cells
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index 4f38dc1..0a1b874 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -109,4 +109,4 @@ vdj_t_cols <- c(
 obs_cols <- c("orig.ident", "nCount_RNA", "nFeature_RNA")
 
 expect_true(all(vdj_t_cols %in% colnames(obj@meta.data)))
-expect_true(all(obs_cols %in% colnames(obj@meta.data)))
\ No newline at end of file
+expect_true(all(obs_cols %in% colnames(obj@meta.data)))

From a339b29910c7b18b27a874ed7caf91f4d398b707 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Thu, 16 Oct 2025 08:13:09 +0200
Subject: [PATCH 05/12] lint

---
 .gitignore                                      |  1 -
 _viash.yaml                                     |  2 +-
 src/convert/from_h5mu_to_seurat/config.vsh.yaml |  4 ++--
 src/convert/from_h5mu_to_seurat/script.R        | 13 ++++++++-----
 src/convert/from_h5mu_to_seurat/test.R          |  2 +-
 5 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/.gitignore b/.gitignore
index 606d4b8..97dc208 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,7 +25,6 @@ out/
 output*
 output_log/
 resources_test
-resources_test_sc
 /viash_tools/
 /test/
 
diff --git a/_viash.yaml b/_viash.yaml
index f64a065..d56fdcf 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -23,7 +23,7 @@ info:
       dest: resources_test
     - type: s3
       path: s3://openpipelines-data
-      dest: resources_test_sc
+      dest: resources_test
 
 config_mods: |
   .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
index 0b9f59b..26f2d0d 100644
--- a/src/convert/from_h5mu_to_seurat/config.vsh.yaml
+++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
@@ -43,8 +43,8 @@ resources:
 test_resources:
   - type: r_script
     path: test.R
-  - path: /resources_test_sc/pbmc_1k_protein_v3/
-  - path: /resources_test_sc/10x_5k_anticmv/
+  - path: /resources_test/pbmc_1k_protein_v3/
+  - path: /resources_test/10x_5k_anticmv/
 engines:
   - type: docker
     image: rocker/r2u:22.04
diff --git a/src/convert/from_h5mu_to_seurat/script.R b/src/convert/from_h5mu_to_seurat/script.R
index 0c780e3..326968c 100644
--- a/src/convert/from_h5mu_to_seurat/script.R
+++ b/src/convert/from_h5mu_to_seurat/script.R
@@ -4,8 +4,8 @@ library(Seurat)
 
 ### VIASH START
 par <- list(
-  input = "resources_test_sc/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect.h5mu",
-  output = "resources_test_sc/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect.rds",
+  input = "./5k_human_antiCMV_T_TBNK_connect.h5mu",
+  output = "./5k_human_antiCMV_T_TBNK_connect.rds",
   assay = c("RNA", "ADT", "TCR"),
   modality = c("rna", "prot", "vdj_t")
 )
@@ -68,11 +68,11 @@ map_obs_to_metadata <- function(adata, seurat_obj, mod, assay) {
   mod_meta <- mod_meta[match(cells, obs_names), , drop = FALSE]
   rownames(mod_meta) <- cells
 
-  seurat_obj <- AddMetaData(seurat_obj, mod_meta)
+  seurat_obj <- Seurat::AddMetaData(seurat_obj, mod_meta)
 }
 
 map_modality_to_assay <- function(adata, seurat_obj, assay) {
-  temp_seurat <- read_h5ad(
+  temp_seurat <- anndatar::read_h5ad(
     adata,
     mode = "r",
     as = "Seurat",
@@ -128,7 +128,10 @@ for (i in seq_along(par$modality)) {
 }
 
 if (is.null(seurat_obj)) {
-  stop("No valid modalities found to create a Seurat object. At least one modality must have non-zero dimensions.")
+  stop(
+    "No valid modalities found to create a Seurat object.",
+    "At least one modality must have non-zero dimensions."
+  )
 }
 
 for (mod in names(modalities_to_metadata)) {
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index 0a1b874..f33740a 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -5,7 +5,7 @@ library(hdf5r)
 ## VIASH START
 meta <- list(
   executable = "target/executable/convert/from_h5ad_to_seurat",
-  resources_dir = "resources_test_sc",
+  resources_dir = "resources_test",
   name = "from_h5ad_to_seurat"
 )
 ## VIASH END

From 6761d44f6f9f814ad0ebab37fd061d118a39b268 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Thu, 16 Oct 2025 09:05:54 +0200
Subject: [PATCH 06/12] lint

---
 src/convert/from_h5mu_to_seurat/script.R |  2 +-
 src/convert/from_h5mu_to_seurat/test.R   | 11 ++++++-----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/convert/from_h5mu_to_seurat/script.R b/src/convert/from_h5mu_to_seurat/script.R
index 326968c..90d483b 100644
--- a/src/convert/from_h5mu_to_seurat/script.R
+++ b/src/convert/from_h5mu_to_seurat/script.R
@@ -72,7 +72,7 @@ map_obs_to_metadata <- function(adata, seurat_obj, mod, assay) {
 }
 
 map_modality_to_assay <- function(adata, seurat_obj, assay) {
-  temp_seurat <- anndatar::read_h5ad(
+  temp_seurat <- anndataR::read_h5ad(
     adata,
     mode = "r",
     as = "Seurat",
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index f33740a..b7795ff 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -100,11 +100,12 @@ vdj_t_cols <- c(
   "TCR_IR_VJ_1_j_call", "TCR_IR_VJ_2_j_call", "TCR_IR_VDJ_1_j_call",
   "TCR_IR_VDJ_2_j_call", "TCR_IR_VJ_1_junction", "TCR_IR_VJ_2_junction",
   "TCR_IR_VDJ_1_junction", "TCR_IR_VDJ_2_junction", "TCR_IR_VJ_1_junction_aa",
-  "TCR_IR_VJ_2_junction_aa", "TCR_IR_VDJ_1_junction_aa", "TCR_IR_VDJ_2_junction_aa",
-  "TCR_IR_VJ_1_locus", "TCR_IR_VJ_2_locus", "TCR_IR_VDJ_1_locus",
-  "TCR_IR_VDJ_2_locus", "TCR_IR_VJ_1_productive", "TCR_IR_VJ_2_productive",
-  "TCR_IR_VDJ_1_productive", "TCR_IR_VDJ_2_productive", "TCR_IR_VJ_1_v_call",
-  "TCR_IR_VJ_2_v_call", "TCR_IR_VDJ_1_v_call", "TCR_IR_VDJ_2_v_call", "TCR_has_ir"
+  "TCR_IR_VJ_2_junction_aa", "TCR_IR_VDJ_1_junction_aa",
+  "TCR_IR_VDJ_2_junction_aa", "TCR_IR_VJ_1_locus", "TCR_IR_VJ_2_locus",
+  "TCR_IR_VDJ_1_locus", "TCR_IR_VDJ_2_locus", "TCR_IR_VJ_1_productive",
+  "TCR_IR_VJ_2_productive", "TCR_IR_VDJ_1_productive",
+  "TCR_IR_VDJ_2_productive", "TCR_IR_VJ_1_v_call", "TCR_IR_VJ_2_v_call",
+  "TCR_IR_VDJ_1_v_call", "TCR_IR_VDJ_2_v_call", "TCR_has_ir"
 )
 obs_cols <- c("orig.ident", "nCount_RNA", "nFeature_RNA")
 

From 801b374cf3752009ccf3f6c50cd7a5632ca84663 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Thu, 16 Oct 2025 09:34:07 +0200
Subject: [PATCH 07/12] rename test resources

---
 _viash.yaml                                     | 2 +-
 src/convert/from_h5mu_to_seurat/config.vsh.yaml | 4 ++--
 src/convert/from_h5mu_to_seurat/test.R          | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/_viash.yaml b/_viash.yaml
index d56fdcf..5eb8ad9 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -23,7 +23,7 @@ info:
       dest: resources_test
     - type: s3
       path: s3://openpipelines-data
-      dest: resources_test
+      dest: op_resources_test
 
 config_mods: |
   .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
index 26f2d0d..d536073 100644
--- a/src/convert/from_h5mu_to_seurat/config.vsh.yaml
+++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
@@ -43,8 +43,8 @@ resources:
 test_resources:
   - type: r_script
     path: test.R
-  - path: /resources_test/pbmc_1k_protein_v3/
-  - path: /resources_test/10x_5k_anticmv/
+  - path: /resources_test_op/pbmc_1k_protein_v3/
+  - path: /resources_test_op/10x_5k_anticmv/
 engines:
   - type: docker
     image: rocker/r2u:22.04
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index b7795ff..89fc149 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -5,7 +5,7 @@ library(hdf5r)
 ## VIASH START
 meta <- list(
   executable = "target/executable/convert/from_h5ad_to_seurat",
-  resources_dir = "resources_test",
+  resources_dir = "op_resources_test",
   name = "from_h5ad_to_seurat"
 )
 ## VIASH END

From 37ca9b9d8504d051ba669ea27276988c0a88ba6f Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Thu, 16 Oct 2025 09:45:31 +0200
Subject: [PATCH 08/12] rename test resources

---
 _viash.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_viash.yaml b/_viash.yaml
index 5eb8ad9..3cf7f6e 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -23,7 +23,7 @@ info:
       dest: resources_test
     - type: s3
       path: s3://openpipelines-data
-      dest: op_resources_test
+      dest: resources_test_op
 
 config_mods: |
   .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}

From 025e6e4a0c717e071e9d29d8d96010afcfb94d7d Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Fri, 17 Oct 2025 12:50:17 +0200
Subject: [PATCH 09/12] add spatial h5mu conversion to seurat

---
 _viash.yaml                                   |   3 -
 .../from_h5mu_to_seurat/config.vsh.yaml       |  97 ++++++----
 src/convert/from_h5mu_to_seurat/script.R      | 124 ++++--------
 src/convert/from_h5mu_to_seurat/test.R        | 182 +++++++++++++-----
 4 files changed, 233 insertions(+), 173 deletions(-)

diff --git a/_viash.yaml b/_viash.yaml
index 3cf7f6e..504fcce 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -21,9 +21,6 @@ info:
     - type: s3
       path: s3://openpipelines-bio/openpipeline_spatial/resources_test
       dest: resources_test
-    - type: s3
-      path: s3://openpipelines-data
-      dest: resources_test_op
 
 config_mods: |
   .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
index d536073..694a2c6 100644
--- a/src/convert/from_h5mu_to_seurat/config.vsh.yaml
+++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
@@ -2,49 +2,73 @@ name: "from_h5mu_to_seurat"
 namespace: "convert"
 scope: "public"
 description: |
-  Converts an h5ad file or a single modality of an h5mu file into a Seurat file.
+  Converts an h5ad file or a single modality of an h5mu file into a Seurat file with a Field of View (FOV) field, 
+  storing coordinates of spatially-resolved single cells based on centroid coordinates.
 authors:
   - __merge__: /src/authors/dorien_roosen.yaml
     roles: [ author, maintainer ]
-arguments:
-  - name: "--input"
-    alternatives: ["-i"]
-    type: file
-    description: Input h5ad or h5mu file
-    direction: input
-    required: true
-    example: input.h5ad
-  - name: "--modality"
-    type: string
-    default: ["rna"]
-    multiple: true
-    example: ["rna", "prot", "vdj"]
-    required: false
-    description: Modality to be converted if the input file is an h5mu file.
-  - name: "--assay"
-    type: string
-    default: ["RNA"]
-    multiple: true
-    example: ["RNA", "ADT", "VDJ"]
-    description: |
-      Name of the assay to be created.
-      Order should match the order of the --modalities.
-      If layer dimensions of a modality are 0, the modality will be moved to the metadata instead of an assay.
-  - name: "--output"
-    alternatives: ["-o"]
-    type: file
-    description: Output Seurat file
-    direction: output
-    required: true
-    example: output.rds
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: "--input"
+      alternatives: ["-i"]
+      type: file
+      description: Input h5ad or h5mu file
+      direction: input
+      required: true
+      example: input.h5ad
+    - name: "--modality"
+      type: string
+      default: "rna"
+      required: true
+      description: Modality to be converted if the input file is an h5mu file.
+    - name: "--obsm_centroid_coordinates"
+      type: string
+      description: |
+        Key name of the .obsm slot in the input file that contains the spatial (centroid) coordinates.
+        If not provided, no Field of View (FOV) will be created in the Seurat object.
+  - name: Centroid arguments
+    arguments:
+    - name: "--centroid_nsides"
+      type: integer
+      required: false
+      description: |
+        Number of sides of the polygon to be created around each centroid coordinate to represent the cell shape.
+        If not provided, circles will be created.
+    - name: "--centroid_radius"
+      type: double
+      required: false
+      description: |
+        Radius of the shape around each centroid coordinate to represent the cell shape.
+        If not provided, a default radius will be calculated based on the provided centroid coordinates.
+    - name: "--centroid_theta"
+      type: double
+      required: false
+      description: |
+        Angle to adjust the shapes around each centroid when plotting.
+        If not provided, no adjustment will be made (theta = 0)
+  - name: Outputs
+    arguments:
+    - name: "--output"
+      alternatives: ["-o"]
+      type: file
+      description: Output Seurat file
+      direction: output
+      required: true
+      example: output.rds
+    - name: "--assay"
+      type: string
+      default: "RNA"
+      description: Name of the assay to be created.
 resources:
   - type: r_script
     path: script.R
 test_resources:
   - type: r_script
     path: test.R
-  - path: /resources_test_op/pbmc_1k_protein_v3/
-  - path: /resources_test_op/10x_5k_anticmv/
+  - path: /resources_test/aviti/aviti_teton_tiny.h5mu
+  - path: /resources_test/cosmx/Lung5_Rep2_tiny.h5mu
+  - path: /resources_test/xenium/xenium_tiny_processed.h5mu
 engines:
   - type: docker
     image: rocker/r2u:22.04
@@ -52,9 +76,8 @@ engines:
       - type: apt
         packages: [ libhdf5-dev, libgeos-dev, hdf5-tools ]
       - type: r
-        cran: [ anndata, hdf5r, Matrix, SeuratObject, Seurat ]
+        cran: [ anndata, hdf5r, Seurat, SeuratObject ]
         github: scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a
-        bioc: [ rhdf5]
     test_setup:
       - type: r
         cran: [ testthat ]
@@ -62,4 +85,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [lowmem, singlecpu]
+      label: [lowmem, singlecpu]
\ No newline at end of file
diff --git a/src/convert/from_h5mu_to_seurat/script.R b/src/convert/from_h5mu_to_seurat/script.R
index 90d483b..0b7b0f5 100644
--- a/src/convert/from_h5mu_to_seurat/script.R
+++ b/src/convert/from_h5mu_to_seurat/script.R
@@ -4,21 +4,24 @@ library(Seurat)
 
 ### VIASH START
 par <- list(
-  input = "./5k_human_antiCMV_T_TBNK_connect.h5mu",
-  output = "./5k_human_antiCMV_T_TBNK_connect.rds",
-  assay = c("RNA", "ADT", "TCR"),
-  modality = c("rna", "prot", "vdj_t")
+  input = "resources_test/xenium/xenium_tiny_processed.h5mu",
+  output = "test.rds",
+  obsm_centroid_coordinates = "spatial",
+  assay = "RNA",
+  centroid_nsides = 8,
+  centroid_radius = 3,
+  centroid_theta = 0.1,
+  modality = "rna"
 )
 ### VIASH END
 
+
 h5mu_to_h5ad <- function(h5mu_path, modality_name) {
   tmp_path <- tempfile(fileext = ".h5ad")
   mod_location <- paste("mod", modality_name, sep = "/")
   h5src <- hdf5r::H5File$new(h5mu_path, "r")
   h5dest <- hdf5r::H5File$new(tmp_path, "w")
   # Copy over the child objects and the child attributes from root
-  # Root cannot be copied directly because it always exists and
-  # copying does not allow overwriting.
   children <- hdf5r::list.objects(h5src,
     path = mod_location,
     full.names = FALSE, recursive = FALSE
@@ -48,96 +51,43 @@ h5mu_to_h5ad <- function(h5mu_path, modality_name) {
   tmp_path
 }
 
-has_zero_dimension <- function(adata) {
-  adata_dims <- adata$shape()
-  any(adata_dims == 0)
-}
-
-map_obs_to_metadata <- function(adata, seurat_obj, mod, assay) {
-  cells <- colnames(seurat_obj)
-  mod_meta <- adata$obs
-  obs_names <- rownames(mod_meta)
-  colnames(mod_meta) <- paste0(assay, "_", make.names(colnames(mod_meta)))
-
-  if (!all(obs_names %in% cells)) {
-    stop(paste0(
-      "Not all cells in the adata modality", mod,
-      "are present in the Seurat object."
-    ))
-  }
-  mod_meta <- mod_meta[match(cells, obs_names), , drop = FALSE]
-  rownames(mod_meta) <- cells
+# Read in H5AD
+h5ad_path <- h5mu_to_h5ad(par$input, par$modality)
 
-  seurat_obj <- Seurat::AddMetaData(seurat_obj, mod_meta)
-}
+# Convert to Seurat
+seurat_obj <- read_h5ad(
+  h5ad_path,
+  mode = "r",
+  as = "Seurat",
+  assay_name = par$assay
+)
 
-map_modality_to_assay <- function(adata, seurat_obj, assay) {
-  temp_seurat <- anndataR::read_h5ad(
-    adata,
-    mode = "r",
-    as = "Seurat",
-    assay_name = assay
-  )
+# Create Centroids object
+if (!is.null(par$obsm_centroid_coordinates)) {
+  reductions <- seurat_obj@reductions[[par$obsm_centroid_coordinates]]
+  spatial_coords <- as.data.frame(reductions@cell.embeddings)
+  colnames(spatial_coords) <- c("x_coord", "y_coord")
 
-  # If this is the first modality, initialize the main Seurat object
-  if (is.null(seurat_obj)) {
-    seurat_obj <- temp_seurat
-  } else {
-    # Add as additional assay to existing Seurat object
-    seurat_obj[[assay]] <- temp_seurat[[assay]]
+  if (is.null(par$centroid_nsides)) {
+    par$centroid_nsides <- Inf
   }
-  seurat_obj
-}
 
-# Initialize seurat object
-seurat_obj <- NULL
-modalities_to_metadata <- list()
-
-# Check that modalities and assays have the same length
-if (length(par$modality) != length(par$assay)) {
-  stop("The number of modalities should match the number of assays.")
-}
-
-# Loop through modalities and assays
-for (i in seq_along(par$modality)) {
-  mod <- par$modality[i]
-  assay <- par$assay[i]
-  cat("Processing modality:", mod, "as assay:", assay, "\n")
-
-  # Read the specific modality from h5mu file
-  adata_path <- h5mu_to_h5ad(par$input, mod)
-  adata <- read_h5ad(adata_path, mode = "r")
-
-  # Check dimensions: modalities with dimension 0 will be added later
-  if (has_zero_dimension(adata)) {
-    if (adata$shape()[1] == 0) {
-      cat("Skipping modality", mod, "- has zero observations\n")
-    } else {
-      cat(
-        "Modality",
-        mod,
-        "has zero features - moving to metadata\n"
-      )
-      modalities_to_metadata[[mod]] <- assay
-    }
-    next
+  if (is.null(par$centroid_theta)) {
+    par$centroid_theta <- 0L
   }
 
-  # Convert to Seurat assay
-  seurat_obj <- map_modality_to_assay(adata_path, seurat_obj, assay)
-}
-
-if (is.null(seurat_obj)) {
-  stop(
-    "No valid modalities found to create a Seurat object.",
-    "At least one modality must have non-zero dimensions."
+  centroids <- CreateCentroids(
+    coords = spatial_coords,
+    nsides = par$centroid_nsides,
+    radius = par$centroid_radius,
+    theta = par$centroid_theta
   )
-}
 
-for (mod in names(modalities_to_metadata)) {
-  assay <- modalities_to_metadata[[mod]]
-  cat("Moving modality", mod, "to metadata\n")
-  seurat_obj <- map_obs_to_metadata(adata, seurat_obj, mod, assay)
+  # Create FOV object
+  fov <- CreateFOV(coords = centroids, assay = par$assay)
+  seurat_obj[["fov"]] <- fov
+  seurat_obj@reductions[[par$obsm_centroid_coordinates]] <- NULL
 }
 
+
 saveRDS(seurat_obj, file = par$output)
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index 89fc149..c70e360 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -1,21 +1,22 @@
 library(testthat, warn.conflicts = FALSE)
 library(hdf5r)
-
+library(Seurat)
 
 ## VIASH START
 meta <- list(
-  executable = "target/executable/convert/from_h5ad_to_seurat",
-  resources_dir = "op_resources_test",
-  name = "from_h5ad_to_seurat"
+  executable = "target/executable/convert/from_h5ad_to_spatial_seurat",
+  resources_dir = "resources_test",
+  name = "from_h5ad_to_spatial_seurat"
 )
 ## VIASH END
 
-## Simple conversion
-cat("> Checking conversion of single-modality of h5mu file\n")
+
+# ---- No FOV ----------------------------------------------------------
+cat("> Test conversion without adding FOV\n")
 
 in_h5mu <- paste0(
   meta[["resources_dir"]],
-  "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
+  "/xenium_tiny_processed.h5mu"
 )
 out_rds <- "output.rds"
 
@@ -24,7 +25,9 @@ out <- processx::run(
   meta[["executable"]],
   c(
     "--input", in_h5mu,
-    "--output", out_rds
+    "--output", out_rds,
+    "--modality", "rna",
+    "--assay", "Xenium"
   )
 )
 
@@ -34,24 +37,26 @@ expect_true(file.exists(out_rds))
 
 cat("> Reading output file\n")
 obj <- readRDS(file = out_rds)
+adata <- H5File$new(in_h5mu, mode = "r")[["/mod/rna/X"]]
 
 cat("> Checking whether Seurat object is in the right format\n")
-expect_is(obj, "Seurat")
-expect_equal(names(slot(obj, "assays")), "RNA")
+expect_equal(Assays(obj), "Xenium")
+expect_true(all(Layers(obj) == c("counts", "log_normalized")))
 
 dim_rds <- dim(obj)
-mu_in <- H5File$new(in_h5mu, mode = "r")
-dim_ad <- mu_in[["/mod/rna/X"]]$attr_open("shape")$read()
+dim_ad <- adata$attr_open("shape")$read()
 
 expect_equal(dim_rds[1], dim_ad[2])
 expect_equal(dim_rds[2], dim_ad[1])
 
-## Multi-modal conversion
-cat("> Checking conversion of multi-modal h5mu file\n")
+expect_false("fov" %in% names(obj))
+
+# # ---- Xenium ----------------------------------------------------------
+cat("> Test conversion Xenium\n")
 
 in_h5mu <- paste0(
   meta[["resources_dir"]],
-  "/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect.h5mu"
+  "/xenium_tiny_processed.h5mu"
 )
 out_rds <- "output.rds"
 
@@ -60,13 +65,10 @@ out <- processx::run(
   meta[["executable"]],
   c(
     "--input", in_h5mu,
+    "--output", out_rds,
     "--modality", "rna",
-    "--modality", "prot",
-    "--modality", "vdj_t",
-    "--assay", "RNA",
-    "--assay", "ADT",
-    "--assay", "TCR",
-    "--output", out_rds
+    "--assay", "Xenium",
+    "--obsm_centroid_coordinates", "spatial"
   )
 )
 
@@ -76,38 +78,126 @@ expect_true(file.exists(out_rds))
 
 cat("> Reading output file\n")
 obj <- readRDS(file = out_rds)
+adata <- H5File$new(in_h5mu, mode = "r")[["/mod/rna/X"]]
 
 cat("> Checking whether Seurat object is in the right format\n")
-expect_is(obj, "Seurat")
-expect_true(all(names(slot(obj, "assays")) %in% c("RNA", "ADT")))
+expect_equal(Assays(obj), "Xenium")
+expect_true(all(Layers(obj) == c("counts", "log_normalized")))
 
 dim_rds <- dim(obj)
-mu_in <- H5File$new(in_h5mu, mode = "r")
-dim_ad <- mu_in[["/mod/rna/X"]]$attr_open("shape")$read()
+dim_ad <- adata$attr_open("shape")$read()
 
 expect_equal(dim_rds[1], dim_ad[2])
 expect_equal(dim_rds[2], dim_ad[1])
 
-vdj_t_cols <- c(
-  "TCR_is_cell", "TCR_high_confidence", "TCR_multi_chain", "TCR_extra_chains",
-  "TCR_IR_VJ_1_c_call", "TCR_IR_VJ_2_c_call", "TCR_IR_VDJ_1_c_call",
-  "TCR_IR_VDJ_2_c_call", "TCR_IR_VJ_1_consensus_count",
-  "TCR_IR_VJ_2_consensus_count", "TCR_IR_VDJ_1_consensus_count",
-  "TCR_IR_VDJ_2_consensus_count", "TCR_IR_VJ_1_d_call",
-  "TCR_IR_VJ_2_d_call", "TCR_IR_VDJ_1_d_call", "TCR_IR_VDJ_2_d_call",
-  "TCR_IR_VJ_1_duplicate_count", "TCR_IR_VJ_2_duplicate_count",
-  "TCR_IR_VDJ_1_duplicate_count", "TCR_IR_VDJ_2_duplicate_count",
-  "TCR_IR_VJ_1_j_call", "TCR_IR_VJ_2_j_call", "TCR_IR_VDJ_1_j_call",
-  "TCR_IR_VDJ_2_j_call", "TCR_IR_VJ_1_junction", "TCR_IR_VJ_2_junction",
-  "TCR_IR_VDJ_1_junction", "TCR_IR_VDJ_2_junction", "TCR_IR_VJ_1_junction_aa",
-  "TCR_IR_VJ_2_junction_aa", "TCR_IR_VDJ_1_junction_aa",
-  "TCR_IR_VDJ_2_junction_aa", "TCR_IR_VJ_1_locus", "TCR_IR_VJ_2_locus",
-  "TCR_IR_VDJ_1_locus", "TCR_IR_VDJ_2_locus", "TCR_IR_VJ_1_productive",
-  "TCR_IR_VJ_2_productive", "TCR_IR_VDJ_1_productive",
-  "TCR_IR_VDJ_2_productive", "TCR_IR_VJ_1_v_call", "TCR_IR_VJ_2_v_call",
-  "TCR_IR_VDJ_1_v_call", "TCR_IR_VDJ_2_v_call", "TCR_has_ir"
+cat("> Checking FOV object\n")
+expect_true("fov" %in% names(obj))
+expect_true("fov" %in% Images(obj))
+
+fov <- obj[["fov"]]
+expect_equal(fov@assay, "Xenium")
+expect_equal(fov@key, "Xenium_")
+
+centroids <- fov@boundaries$centroids
+expect_equal(nrow(centroids@coords), dim_rds[2])
+
+centroid_coords <- centroids@coords
+expect_true(is.numeric(centroid_coords[, 1]))
+expect_true(is.numeric(centroid_coords[, 2]))
+expect_false(any(is.na(centroid_coords)))
+
+# # ---- Xenium with args-------------------------------------------------
+cat("> Test conversion Xenium with centroid arguments\n")
+
+in_h5mu <- paste0(
+  meta[["resources_dir"]],
+  "/xenium_tiny_processed.h5mu"
+)
+out_rds <- "output.rds"
+
+cat("> Running ", meta[["name"]], "\n", sep = "")
+out <- processx::run(
+  meta[["executable"]],
+  c(
+    "--input", in_h5mu,
+    "--output", out_rds,
+    "--modality", "rna",
+    "--assay", "Xenium",
+    "--obsm_centroid_coordinates", "spatial",
+    "--centroid_nsides", "8",
+    "--centroid_radius", "3",
+    "--centroid_theta", "0.1"
+  )
 )
-obs_cols <- c("orig.ident", "nCount_RNA", "nFeature_RNA")
 
-expect_true(all(vdj_t_cols %in% colnames(obj@meta.data)))
-expect_true(all(obs_cols %in% colnames(obj@meta.data)))
+cat("> Checking whether output file exists\n")
+expect_equal(out$status, 0)
+expect_true(file.exists(out_rds))
+
+cat("> Reading output file\n")
+obj <- readRDS(file = out_rds)
+adata <- H5File$new(in_h5mu, mode = "r")[["/mod/rna/X"]]
+
+cat("> Checking FOV object\n")
+fov <- obj[["fov"]]
+centroids <- fov@boundaries$centroids
+expect_equal(centroids@nsides, 8)
+expect_equal(centroids@radius, 3)
+expect_equal(centroids@theta, 0.1)
+
+
+# ---- CosMx ----------------------------------------------------------
+
+cat("> Test conversion CosMx\n")
+
+in_h5mu <- paste0(
+  meta[["resources_dir"]],
+  "/Lung5_Rep2_tiny.h5mu"
+)
+out_rds <- "output.rds"
+
+cat("> Running ", meta[["name"]], "\n", sep = "")
+out <- processx::run(
+  meta[["executable"]],
+  c(
+    "--input", in_h5mu,
+    "--output", out_rds,
+    "--modality", "rna",
+    "--assay", "CosMx",
+    "--obsm_centroid_coordinates", "spatial"
+  )
+)
+
+cat("> Checking whether output file exists\n")
+expect_equal(out$status, 0)
+expect_true(file.exists(out_rds))
+
+cat("> Reading output file\n")
+obj <- readRDS(file = out_rds)
+adata <- H5File$new(in_h5mu, mode = "r")[["/mod/rna/X"]]
+
+cat("> Checking whether Seurat object is in the right format\n")
+expect_equal(Assays(obj), "CosMx")
+expect_true(all(Layers(obj) == c("counts")))
+
+dim_rds <- dim(obj)
+dim_ad <- adata$attr_open("shape")$read()
+
+expect_equal(dim_rds[1], dim_ad[2])
+expect_equal(dim_rds[2], dim_ad[1])
+
+cat("> Checking FOV object\n")
+expect_true("fov" %in% names(obj))
+expect_true("fov" %in% Images(obj))
+
+fov <- obj[["fov"]]
+expect_equal(fov@assay, "CosMx")
+expect_equal(fov@key, "CosMx_")
+
+centroids <- fov@boundaries$centroids
+expect_equal(nrow(centroids@coords), dim_rds[2])
+
+centroid_coords <- centroids@coords
+expect_true(is.numeric(centroid_coords[, 1]))
+expect_true(is.numeric(centroid_coords[, 2]))
+expect_false(any(is.na(centroid_coords)))

From 076d035daf1125be46d73418e4c119990caaeb94 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Fri, 17 Oct 2025 13:19:04 +0200
Subject: [PATCH 10/12] update test resources

---
 src/convert/from_h5mu_to_seurat/config.vsh.yaml |  2 +-
 src/convert/from_h5mu_to_seurat/test.R          | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
index 694a2c6..c8e23c2 100644
--- a/src/convert/from_h5mu_to_seurat/config.vsh.yaml
+++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml
@@ -68,7 +68,7 @@ test_resources:
     path: test.R
   - path: /resources_test/aviti/aviti_teton_tiny.h5mu
   - path: /resources_test/cosmx/Lung5_Rep2_tiny.h5mu
-  - path: /resources_test/xenium/xenium_tiny_processed.h5mu
+  - path: /resources_test/xenium/xenium_tiny.h5mu
 engines:
   - type: docker
     image: rocker/r2u:22.04
diff --git a/src/convert/from_h5mu_to_seurat/test.R b/src/convert/from_h5mu_to_seurat/test.R
index c70e360..9cae0ea 100644
--- a/src/convert/from_h5mu_to_seurat/test.R
+++ b/src/convert/from_h5mu_to_seurat/test.R
@@ -16,7 +16,7 @@ cat("> Test conversion without adding FOV\n")
 
 in_h5mu <- paste0(
   meta[["resources_dir"]],
-  "/xenium_tiny_processed.h5mu"
+  "/xenium_tiny.h5mu"
 )
 out_rds <- "output.rds"
 
@@ -41,7 +41,7 @@ adata <- H5File$new(in_h5mu, mode = "r")[["/mod/rna/X"]]
 
 cat("> Checking whether Seurat object is in the right format\n")
 expect_equal(Assays(obj), "Xenium")
-expect_true(all(Layers(obj) == c("counts", "log_normalized")))
+expect_true(all(Layers(obj) == c("counts")))
 
 dim_rds <- dim(obj)
 dim_ad <- adata$attr_open("shape")$read()
@@ -56,7 +56,7 @@ cat("> Test conversion Xenium\n")
 
 in_h5mu <- paste0(
   meta[["resources_dir"]],
-  "/xenium_tiny_processed.h5mu"
+  "/xenium_tiny.h5mu"
 )
 out_rds <- "output.rds"
 
@@ -82,7 +82,7 @@ adata <- H5File$new(in_h5mu, mode = "r")[["/mod/rna/X"]]
 
 cat("> Checking whether Seurat object is in the right format\n")
 expect_equal(Assays(obj), "Xenium")
-expect_true(all(Layers(obj) == c("counts", "log_normalized")))
+expect_true(all(Layers(obj) == c("counts")))
 
 dim_rds <- dim(obj)
 dim_ad <- adata$attr_open("shape")$read()
@@ -111,7 +111,7 @@ cat("> Test conversion Xenium with centroid arguments\n")
 
 in_h5mu <- paste0(
   meta[["resources_dir"]],
-  "/xenium_tiny_processed.h5mu"
+  "/xenium_tiny.h5mu"
 )
 out_rds <- "output.rds"
 

From d6ec5d9ad1f980c9ecd76bdb19e02ff1ba3e1a94 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Fri, 17 Oct 2025 13:23:09 +0200
Subject: [PATCH 11/12] undo irrelevant changes

---
 src/convert/from_xenium_to_spatialexperiment/script.R | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/convert/from_xenium_to_spatialexperiment/script.R b/src/convert/from_xenium_to_spatialexperiment/script.R
index 5c46b1f..16cf22f 100644
--- a/src/convert/from_xenium_to_spatialexperiment/script.R
+++ b/src/convert/from_xenium_to_spatialexperiment/script.R
@@ -2,7 +2,7 @@ library(SpatialExperimentIO)
 
 ### VIASH START
 par <- list(
-  input = "output-XETG00150__0031015__slidearray0085__20241023__195946",
+  input = "resources_test/xenium/temp_dir.zip",
   add_experiment_xenium = TRUE,
   add_parquet_paths = TRUE,
   alternative_experiment_features = c(
@@ -46,9 +46,7 @@ spe <- readXeniumSXE(
   coordNames = c("x_centroid", "y_centroid"),
   addExperimentXenium = par$add_experiment_xenium,
   addParquetPaths = par$add_parquet_paths,
-  altExps = par$alternative_experiment_features,
-  addCellBound = TRUE,
-  addNucBound = TRUE
+  altExps = par$alternative_experiment_features
 )
 
 cat("Saving output...")

From 3b5314b60d9b8492125d5a7ef51675a62385af6c Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Fri, 17 Oct 2025 13:24:38 +0200
Subject: [PATCH 12/12] update changelog

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0caf808..c597df6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# openpipeline_spatial x.x.x
+
+## NEW FUNCTIONALITY
+
+* `convert/from_h5mu_to_seurat`: Added converter component for H5MU data to Seurat objects with spatial FOV (PR #23).
+
 # openpipeline_spatial 0.1.1
 
 ## MINOR CHANGES