diff --git a/modules/nf-core/xeniumranger/.gitignore b/modules/nf-core/xeniumranger/.gitignore
deleted file mode 100644
index e69de29bb2d1..000000000000
diff --git a/modules/nf-core/xeniumranger/Dockerfile b/modules/nf-core/xeniumranger/Dockerfile
index daa3c965c5e0..1bcc0aad53a6 100644
--- a/modules/nf-core/xeniumranger/Dockerfile
+++ b/modules/nf-core/xeniumranger/Dockerfile
@@ -10,20 +10,20 @@ RUN apt-get update --allow-releaseinfo-change \
 
 # copy over xeniumranger
 # the latest version of the xeniumranger tool has been downloaded from https://www.10xgenomics.com/support/software/xenium-ranger/downloads
-COPY xeniumranger-3.0.1.tar.gz /xeniumranger-3.0.1.tar.gz
+COPY xeniumranger-4.0.0.tar.gz /xeniumranger-4.0.0.tar.gz
 
 # install xenium ranger
-RUN tar -xzvf /xeniumranger-3.0.1.tar.gz && \
-    rm /xeniumranger-3.0.1.tar.gz
+RUN tar -xzvf /xeniumranger-4.0.0.tar.gz && \
+    rm /xeniumranger-4.0.0.tar.gz
 
 # Set environment variables
-# ENV PATH="xeniumranger-xenium3.0/bin:$PATH"
+# ENV PATH="xeniumranger-xenium4.0/bin:$PATH"
 
 # multistage to reduce image size
 FROM ubuntu:20.04
 
 # Set environment variables
-ENV PATH="/xeniumranger-xenium3.0/bin:$PATH"
+ENV PATH="/xeniumranger-xenium4.0/bin:$PATH"
 
 # copy over xenium from builder
-COPY --from=builder /xeniumranger-xenium3.0 /xeniumranger-xenium3.0/
+COPY --from=builder /xeniumranger-xenium4.0 /xeniumranger-xenium4.0/
diff --git a/modules/nf-core/xeniumranger/README.md b/modules/nf-core/xeniumranger/README.md
index 9bbe56b01c29..fbfdb0173f24 100644
--- a/modules/nf-core/xeniumranger/README.md
+++ b/modules/nf-core/xeniumranger/README.md
@@ -5,7 +5,7 @@ Xenium Ranger is a commercial tool from 10X Genomics. The container provided for
 1. Navigate to the appropriate download page. - [Xenium Ranger](https://www.10xgenomics.com/support/software/xenium-ranger/downloads): download the tar ball of the desired Xenium Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
 
 2. Edit the Dockerfile. Update the Xenium Ranger versions in this line:
-   (current version for xenium ranger is fixated at [3.0.1](https://www.10xgenomics.com/support/software/xenium-ranger/downloads) in the dockerfile)
+   (current version for xenium ranger is fixated at [4.0.0](https://www.10xgenomics.com/support/software/xenium-ranger/downloads) in the dockerfile)
 
 3. Create and test the container:
 
diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf
index 50b17272a16c..264b8a72ef63 100644
--- a/modules/nf-core/xeniumranger/import-segmentation/main.nf
+++ b/modules/nf-core/xeniumranger/import-segmentation/main.nf
@@ -2,80 +2,67 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/xeniumranger:3.0.1"
+    container "nf-core/xeniumranger:4.0"
 
     input:
-    tuple val(meta), path(xenium_bundle)
-    val(expansion_distance)
-    path(coordinate_transform)
-    path(nuclei)
-    path(cells)
-    path(transcript_assignment)
-    path(viz_polygons)
+    tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform), val(units)
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
-    path "versions.yml", emit: versions
+    tuple val(meta), path("${prefix}"), emit: outs
+    tuple val("${task.process}"), val("xeniumranger"), eval("xeniumranger -V | sed -e 's/.*xenium-//'"), emit: versions_xeniumranger, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+        error "XENIUMRANGER_IMPORT_SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
 
-    // image based segmentation options
-    def expansion_distance = expansion_distance ? "--expansion-distance=\"${expansion_distance}\"": "" // expansion distance (default - 5, range - 0 - 100)
-    def coordinate_transform = coordinate_transform ? "--coordinate-transform=\"${coordinate_transform}\"": ""
+    prefix = task.ext.prefix ?: "${meta.id}"
 
-    def nuclei_detection = nuclei ? "--nuclei=\"${nuclei}\"": ""
-    def cells = cells ? "--cells=\"${cells}\"": ""
+    // nuclei and cells are for image segmentation results
+    // transcript_assignment and viz_polygons are for transcript assignment results
+    // they are mutually exclusive
+    if ((nuclei || cells) && (transcript_assignment || viz_polygons)) {
+        error "--nuclei and --cells are for image segmentation results, which are mutually exclusive with --transcript-assignment and --viz-polygons for transcript assignment results. Please use only one of them."
+    }
 
-    // transcript based segmentation
-    def transcript_assignment = transcript_assignment ? "--transcript-assignment=\"${transcript_assignment}\"": ""
-    def viz_polygons = viz_polygons ? "--viz-polygons=\"${viz_polygons}\"":""
+    def assembled_args = []
+    if (task.ext.args) { assembled_args << task.ext.args.trim() }
+    if (nuclei) { assembled_args << "--nuclei=\"${nuclei}\"" }
+    if (cells) { assembled_args << "--cells=\"${cells}\"" }
+    if (transcript_assignment) { assembled_args << "--transcript-assignment=\"${transcript_assignment}\"" }
+    if (viz_polygons) { assembled_args << "--viz-polygons=\"${viz_polygons}\"" }
+    if (coordinate_transform) {
+        assembled_args << "--coordinate-transform=\"${coordinate_transform}\""
+        // if coordinate_transform is provided, units must be microns
+        assembled_args << "--units=\"microns\""
+    } else if (units) {
+        assembled_args << "--units=\"${units}\""
+    }
 
-    // shared argument
-    def units = coordinate_transform ? "--units=microns": "--units=pixels"
+    def args = assembled_args ? assembled_args.join(" \\\n        ") : ""
 
     """
     xeniumranger import-segmentation \\
-        --id="${prefix}" \\
+        --id="XENIUMRANGER_IMPORT_SEGMENTATION" \\
         --xenium-bundle="${xenium_bundle}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
-        ${coordinate_transform} \\
-        ${nuclei_detection} \\
-        ${cells} \\
-        ${expansion_distance} \\
-        ${transcript_assignment} \\
-        ${viz_polygons} \\
-        ${units} \\
         ${args}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    rm -rf "${prefix}"
+    mv XENIUMRANGER_IMPORT_SEGMENTATION/outs "${prefix}"
     """
 
     stub:
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir -p "${prefix}/outs/"
-    touch "${prefix}/outs/fake_file.txt"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    mkdir -p "${prefix}"
+    touch "${prefix}/experiment.xenium"
     """
+
 }
diff --git a/modules/nf-core/xeniumranger/import-segmentation/meta.yml b/modules/nf-core/xeniumranger/import-segmentation/meta.yml
index 5aefa1c61087..e222df582a05 100644
--- a/modules/nf-core/xeniumranger/import-segmentation/meta.yml
+++ b/modules/nf-core/xeniumranger/import-segmentation/meta.yml
@@ -1,9 +1,14 @@
 name: xeniumranger_import_segmentation
-description: The xeniumranger import-segmentation module allows you to specify 2D
-  nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate
-  all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation
-  results can be generated by community-developed tools or prior Xenium segmentation
-  result.
+description: |
+  The xeniumranger import-segmentation module runs `xeniumranger import-segmentation`
+  to recompute Xenium Onboard Analysis outputs using external segmentation results.
+  It supports two execution modes mirroring the Xenium Ranger CLI: an image-based
+  mode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together
+  with optional coordinate transforms and unit definitions, and a transcript-based
+  mode that ingests Baysor-style transcript assignment CSV files plus visualization
+  polygons. Use the image-based inputs when providing label masks or polygons, or
+  switch to the transcript-based inputs when supplying transcript-level assignments
+  so the appropriate command-line arguments are passed to Xenium Ranger.
 keywords:
   - spatial
   - segmentation
@@ -28,66 +33,109 @@ input:
         type: map
         description: |
           Groovy Map containing run information
-          e.g. [id:'xenium_bundle_path']
+          e.g. [ id:'xenium_sample' ]
     - xenium_bundle:
         type: directory
-        description: Path to the xenium output bundle generated by the Xenium Onboard
-          Analysis pipeline
-  - expansion_distance:
-      type: integer
-      description: Nuclei boundary expansion distance in µm. Only for use when nucleus
-        segmentation provided as input. Default-5 (accepted range 0 - 100)
-  - coordinate_transform:
-      type: file
-      description: Image alignment file containing similarity transform matrix e.g.,
-        the _imagealignment.csv file exported from Xenium Explorer
-      ontologies: []
-  - nuclei:
-      type: file
-      description: |
-        Label mask (TIFF or NPY), polygons of nucleus segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the nucleus masks as input).
-        --nuclei will use nucleusGeometry polygon if it exists in the GeoJSON (i.e., for QuPath-like GeoJSON files),
-        or geometry if it does not. Error if --transcript-assignment argument is used.
-      ontologies: []
-  - cells:
-      type: file
-      description: |
-        Label mask (TIFF or NPY), polygons of cell segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the cell masks as input).
-        Features with a non-cell objectType will be ignored. Error if --transcript-assignment argument is used.
-        In Xenium Ranger v2.0, --nuclei no longer needs to be used with --cells.
-      ontologies: []
-  - transcript_assignment:
-      type: file
-      description: |
-        Transcript CSV with cell assignment from Baysor v0.6. Error if --cells or --nuclei arguments are used.
-      ontologies: []
-  - viz_polygons:
-      type: file
-      description: |
-        Cell boundary polygons (GeoJSON) for visualization from Baysor v0.6. Required if --transcript-assignment argument used. Error if --cells or --nuclei arguments used.
-      ontologies: []
+        description: Path to the Xenium output bundle generated by the Xenium
+          Onboard Analysis pipeline
+    - transcript_assignment:
+        type: file
+        optional: true
+        description: |
+          Transcript assignment CSV with cell assignment, such as from Baysor v0.6, (transcript-based mode).
+          Mutually exclusive with image-based inputs (`nuclei`, `cells`). Required when using
+          transcript-based mode. Passed to `--transcript-assignment`.
+        pattern: "*.csv"
+        ontologies:
+          - edam: http://edamontology.org/format_3752 # CSV
+    - viz_polygons:
+        type: file
+        optional: true
+        description: |
+          Cell boundary polygons (GeoJSON) for visualization, such as from Baysor v0.6 (transcript-based mode).
+          Mutually exclusive with image-based inputs (`nuclei`, `cells`). Required when using
+          `transcript_assignment`. Passed to `--viz-polygons`.
+        pattern: "*.{json,geojson}"
+        ontologies:
+          - edam: http://edamontology.org/format_3464 # JSON
+    - nuclei:
+        type: file
+        optional: true
+        description: |
+          Nucleus segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard
+          Analysis cells.zarr.zip (image-based mode).
+          Mutually exclusive with transcript-based inputs
+          (`transcript_assignment`, `viz_polygons`). Passed to `--nuclei`.
+        pattern: "*.{tif,tiff,npy,json,geojson,zarr.zip}"
+        ontologies:
+          - edam: http://edamontology.org/format_4003 # NumPy format
+          - edam: http://edamontology.org/format_3464 # JSON
+    - cells:
+        type: file
+        optional: true
+        description: |
+          Cell segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard
+          Analysis cells.zarr.zip (image-based mode).
+          Mutually exclusive with transcript-based inputs
+          (`transcript_assignment`, `viz_polygons`). Passed to `--cells`.
+        pattern: "*.{tif,tiff,npy,json,geojson,zarr.zip}"
+        ontologies:
+          - edam: http://edamontology.org/format_4003 # NumPy format
+          - edam: http://edamontology.org/format_3464 # JSON
+    - coordinate_transform:
+        type: file
+        optional: true
+        description: |
+          Image alignment file containing similarity transform matrix (e.g., `_imagealignment.csv` from
+          Xenium Explorer). Only used with image-based mode inputs (`nuclei`, `cells`). `units` will be automatically set to "microns". Passed to `--coordinate-transform`.
+        pattern: "*.csv"
+        ontologies:
+          - edam: http://edamontology.org/format_3752 # CSV
+    - units:
+        type: string
+        optional: true
+        description: |
+          Units for segmentation results. Must be one of two options: "microns" (physical space) or
+          "pixels" (pixel space). Can be used with both image-based and transcript-based modes.
+          Default: "pixels". Must be "microns" if `coordinate_transform` is used. For Baysor v0.6
+          inputs, must be "microns". Passed to `--units`.
+        enum:
+          - "microns"
+          - "pixels"
 output:
   outs:
     - - meta:
-          type: file
-          description: Files containing the outputs of Cell Ranger, see official 10X
-            Genomics documentation for a complete list
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
-      - "**/outs/**":
-          type: file
-          description: Files containing the outputs of xenium ranger, see official 10X
-            Genomics documentation for a complete list of outputs
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
+          type: map
+          description: Groovy Map containing sample information e.g. [ id:'test' ]
+      - ${prefix}:
+          type: directory
+          description: Directory containing the output xenium bundle of Xenium
+            Ranger
+          pattern: "${prefix}"
+  versions_xeniumranger:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - xeniumranger -V | sed -e 's/.*xenium-//':
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - xeniumranger -V | sed -e 's/.*xenium-//':
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@khersameesh24"
+  - "@dongzehe"
 maintainers:
   - "@khersameesh24"
+  - "@dongzehe"
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
index 6e2826eba480..3a8616c1c470 100644
--- a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process XENIUMRANGER_IMPORT_SEGMENTATION"
     script "../main.nf"
     process "XENIUMRANGER_IMPORT_SEGMENTATION"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -11,296 +10,70 @@ nextflow_process {
     tag "xeniumranger/import-segmentation"
     tag "unzip"
 
+
     setup {
-            run("UNZIP") {
-                script "modules/nf-core/unzip/main.nf"
-                process {
-                    """
-                    input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)]
-                    """
-                }
-            }
-    }
 
-    test("xeniumranger import-segmentation nuclei npy") {
-        when {
+        run("UNZIP") {
+            script "modules/nf-core/unzip/main.nf"
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_import-segmentation"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = 0
-                input[2] = []
-                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/nuclei.npy"
-                input[4] = []
-                input[5] = []
-                input[6] = []
+                input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip', checkIfExists: true)]
                 """
             }
         }
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.versions,
-                    process.out.outs.get(0).get(1).findAll { file(it).name !in [
-                        'analysis_summary.html',
-                        'metrics_summary.csv',
-                        'cell_boundaries.csv.gz',
-                        'cell_boundaries.parquet',
-                        'nucleus_boundaries.csv.gz',
-                        'nucleus_boundaries.parquet',
-                        'cells.csv.gz',
-                        'cells.parquet',
-                        'cells.zarr.zip',
-                        'transcripts.parquet',
-                        'transcripts.zarr.zip',
-                        'clusters.csv',
-                        'differential_expression.csv',
-                        'components.csv',
-                        'projection.csv',
-                        'variance.csv',
-                        'analysis.zarr.zip',
-                        'experiment.xenium',
-                        'cell_feature_matrix.zarr.zip'
-                        ]}
-                    ).match()
-                },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'differential_expression.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'components.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'projection.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() },
-            )
-        }
-    }
-
 
-    test("xeniumranger import-segmentation nuclei tif") {
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_import-segmentation"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = 0
-                input[2] = []
-                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/nuclei.npy"
-                input[4] = []
-                input[5] = []
-                input[6] = []
-                """
-            }
-        }
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.versions,
-                    process.out.outs.get(0).get(1).findAll { file(it).name !in [
-                        'analysis_summary.html',
-                        'metrics_summary.csv',
-                        'cell_boundaries.csv.gz',
-                        'cell_boundaries.parquet',
-                        'nucleus_boundaries.csv.gz',
-                        'nucleus_boundaries.parquet',
-                        'cells.csv.gz',
-                        'cells.parquet',
-                        'cells.zarr.zip',
-                        'transcripts.parquet',
-                        'transcripts.zarr.zip',
-                        'clusters.csv',
-                        'differential_expression.csv',
-                        'components.csv',
-                        'projection.csv',
-                        'variance.csv',
-                        'analysis.zarr.zip',
-                        'experiment.xenium',
-                        'cell_feature_matrix.zarr.zip'
-                        ]}
-                    ).match()
-                },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'differential_expression.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'components.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'projection.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() },
-            )
-        }
     }
 
-    test("xeniumranger import-segmentation segmentation csv") {
+    test("xeniumranger import-segmentation nuclei") {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_import-segmentation"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = 0
-                input[2] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/imagealignment.csv"
-                input[3] = []
-                input[4] = []
-                input[5] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/segmentation.csv"
-                input[6] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/segmentation_polygons.json"
+                input[0] = UNZIP.out.unzipped_archive
+                    .map { _, bundle ->
+                        [
+                            [id: "test_xeniumranger_import-segmentation"],
+                            bundle,
+                            [],
+                            [],
+                            bundle + "/cells.zarr.zip",
+                            [],
+                            [],
+                            []
+                        ]
+                    }
                 """
             }
         }
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.versions,
-                    process.out.outs.get(0).get(1).findAll { file(it).name !in [
-                        'analysis_summary.html',
-                        'metrics_summary.csv',
-                        'cell_boundaries.csv.gz',
-                        'cell_boundaries.parquet',
-                        'nucleus_boundaries.csv.gz',
-                        'nucleus_boundaries.parquet',
-                        'cells.csv.gz',
-                        'cells.parquet',
-                        'cells.zarr.zip',
-                        'transcripts.parquet',
-                        'transcripts.zarr.zip',
-                        'clusters.csv',
-                        'differential_expression.csv',
-                        'components.csv',
-                        'projection.csv',
-                        'variance.csv',
-                        'analysis.zarr.zip',
-                        'experiment.xenium',
-                        'cell_feature_matrix.zarr.zip'
-                        ]}
-                    ).match()
-                },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'differential_expression.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'components.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'projection.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() },
-            )
-        }
-    }
 
-    test("xeniumranger import-segmentation") {
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_import-segmentation"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = 0
-                input[2] = []
-                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/cells.zarr.zip"
-                input[4] = []
-                input[5] = []
-                input[6] = []
-                """
-            }
-        }
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.versions,
-                    process.out.outs.get(0).get(1).findAll { file(it).name !in [
-                        'analysis_summary.html',
-                        'metrics_summary.csv',
-                        'cell_boundaries.csv.gz',
-                        'cell_boundaries.parquet',
-                        'nucleus_boundaries.csv.gz',
-                        'nucleus_boundaries.parquet',
-                        'cells.csv.gz',
-                        'cells.parquet',
-                        'cells.zarr.zip',
-                        'transcripts.parquet',
-                        'transcripts.zarr.zip',
-                        'clusters.csv',
-                        'differential_expression.csv',
-                        'components.csv',
-                        'projection.csv',
-                        'variance.csv',
-                        'analysis.zarr.zip',
-                        'experiment.xenium',
-                        'cell_feature_matrix.zarr.zip'
-                        ]}
-                    ).match()
-                },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'nucleus_boundaries.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'differential_expression.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'components.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'projection.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() },
+                { assert process.out.outs != null },
+                { assert file(process.out.outs.get(0).get(1)).isDirectory() },
+                { assert file(process.out.outs.get(0).get(1)).list().size() > 0 },
+                { assert snapshot(process.out.versions_xeniumranger).match()},
             )
         }
     }
 
     test("xeniumranger import-segmentation stub") {
         options "-stub"
+
         when {
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_import-segmentation"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = 0
-                input[2] = []
-                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/cells.zarr.zip"
-                input[4] = []
-                input[5] = []
-                input[6] = []
+                input[0] = UNZIP.out.unzipped_archive
+                    .map { _, bundle ->
+                        [
+                            [id: "test_xeniumranger_import-segmentation"],
+                            bundle,
+                            [],
+                            [],
+                            bundle + "/cells.zarr.zip",
+                            [],
+                            []
+                        ]
+                    }
                 """
             }
         }
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap
index 1c312ae0f3ba..b0f079b96e1e 100644
--- a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap
+++ b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap
@@ -1,72 +1,19 @@
 {
-    "xeniumranger import-segmentation": {
+    "xeniumranger import-segmentation nuclei": {
         "content": [
             [
-                "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
-            ],
-            [
-                "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4",
-                "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00",
-                "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6",
-                "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582",
-                "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e",
-                "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1",
-                "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
-                "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-30T00:13:13.575888"
-    },
-    "xeniumranger import-segmentation nuclei npy": {
-        "content": [
-            [
-                "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
-            ],
-            [
-                "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4",
-                "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00",
-                "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6",
-                "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582",
-                "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e",
-                "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1",
-                "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
-                "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-29T23:03:26.726334"
-    },
-    "xeniumranger import-segmentation segmentation csv": {
-        "content": [
-            [
-                "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
-            ],
-            [
-                "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4",
-                "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00",
-                "cell_feature_matrix.h5:md5,5d74ea595561e0300b6c3e5ec8d06fff",
-                "barcodes.tsv.gz:md5,97496a9b448d9380cff0575b8e7a6f57",
-                "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e",
-                "matrix.mtx.gz:md5,f93ed82a2a74c154392fc6237642f1d2",
-                "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
-                "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98"
+                [
+                    "XENIUMRANGER_IMPORT_SEGMENTATION",
+                    "xeniumranger",
+                    "4.0.1.1"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-10-29T23:22:58.158857"
+        "timestamp": "2025-12-10T19:58:12.844137213"
     },
     "xeniumranger import-segmentation stub": {
         "content": [
@@ -76,52 +23,41 @@
                         {
                             "id": "test_xeniumranger_import-segmentation"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
+                    [
+                        "XENIUMRANGER_IMPORT_SEGMENTATION",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ],
                 "outs": [
                     [
                         {
                             "id": "test_xeniumranger_import-segmentation"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
+                "versions_xeniumranger": [
+                    [
+                        "XENIUMRANGER_IMPORT_SEGMENTATION",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-30T22:49:39.204133"
-    },
-    "xeniumranger import-segmentation nuclei tif": {
-        "content": [
-            [
-                "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
-            ],
-            [
-                "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4",
-                "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00",
-                "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6",
-                "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582",
-                "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e",
-                "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1",
-                "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
-                "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-10-29T23:11:37.18721"
+        "timestamp": "2025-12-10T19:58:19.883560548"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/nextflow.config b/modules/nf-core/xeniumranger/import-segmentation/tests/nextflow.config
deleted file mode 100644
index e69de29bb2d1..000000000000
diff --git a/modules/nf-core/xeniumranger/relabel/main.nf b/modules/nf-core/xeniumranger/relabel/main.nf
index b06fe9ea13eb..bf04a9713ec6 100644
--- a/modules/nf-core/xeniumranger/relabel/main.nf
+++ b/modules/nf-core/xeniumranger/relabel/main.nf
@@ -2,55 +2,46 @@ process XENIUMRANGER_RELABEL {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/xeniumranger:3.0.1"
+    container "nf-core/xeniumranger:4.0"
 
     input:
-    tuple val(meta), path(xenium_bundle)
-    path(gene_panel)
+    tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(panel)
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
-    path "versions.yml", emit: versions
+    tuple val(meta), path("${prefix}"), emit: outs
+    tuple val("${task.process}"), val("xeniumranger"), eval("xeniumranger -V | sed -e 's/.*xenium-//'"), emit: versions_xeniumranger, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "XENIUMRANGER_RELABEL module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
 
     """
     xeniumranger relabel \\
-        --id="${prefix}" \\
+        --id="XENIUMRANGER_RELABEL" \\
         --xenium-bundle="${xenium_bundle}" \\
-        --panel="${gene_panel}" \\
+        --panel="${panel}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         ${args}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    rm -rf "${prefix}"
+    mv XENIUMRANGER_RELABEL/outs "${prefix}"
     """
 
     stub:
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "XENIUMRANGER_RELABEL module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    mkdir -p "${prefix}/outs/"
-    touch "${prefix}/outs/fake_file.txt"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    """
+    mkdir -p "${prefix}"
+    touch "${prefix}/experiment.xenium"
     """
 }
diff --git a/modules/nf-core/xeniumranger/relabel/meta.yml b/modules/nf-core/xeniumranger/relabel/meta.yml
index 1d4d263bf214..8b61e0bb8f02 100644
--- a/modules/nf-core/xeniumranger/relabel/meta.yml
+++ b/modules/nf-core/xeniumranger/relabel/meta.yml
@@ -1,6 +1,6 @@
 name: xeniumranger_relabel
-description: The xeniumranger relabel module allows you to change the gene labels
-  applied to decoded transcripts.
+description: The xeniumranger relabel module allows you to change the gene
+  labels applied to decoded transcripts.
 keywords:
   - spatial
   - relabel
@@ -15,44 +15,58 @@ tools:
       documentation: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started"
       tool_dev_url: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis"
       licence:
-        - 10x Genomics EULA
+        - "10x Genomics EULA"
       identifier: ""
 input:
   - - meta:
         type: map
         description: |
           Groovy Map containing run information
-          e.g. [id:'xenium_bundle_path']
+          e.g. [ id:'xenium_bundle_path' ]
     - xenium_bundle:
         type: directory
-        description: Path to the xenium output bundle generated by the Xenium Onboard
-          Analysis pipeline
-  - gene_panel:
-      type: file
-      description: Gene panel JSON file to use for relabeling decoded transcripts
-      ontologies: []
+        description: Path to the xenium output bundle generated by the Xenium
+          Onboard Analysis pipeline
+    - panel:
+        type: file
+        description: Path to the gene panel file
+        pattern: "*.json"
+        ontologies:
+          - edam: http://edamontology.org/format_3464 # JSON
 output:
   outs:
     - - meta:
-          type: file
-          description: Files containing the outputs of Cell Ranger, see official 10X
-            Genomics documentation for a complete list
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
-      - "**/outs/**":
-          type: file
-          description: Files containing the outputs of xenium ranger, see official 10X
-            Genomics documentation for a complete list of outputs
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
+          type: map
+          description: Groovy Map containing sample information e.g. [ id:'test' ]
+      - "${prefix}":
+          type: directory
+          description: Directory containing the output xenium bundle of Xenium
+            Ranger
+          pattern: "${prefix}"
+  versions_xeniumranger:
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/.*xenium-//'":
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/.*xenium-//'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@khersameesh24"
+  - "@dongzehe"
 maintainers:
   - "@khersameesh24"
+  - "@dongzehe"
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
index 9db6e96a62f1..6518e8b8214d 100644
--- a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process XENIUMRANGER_RELABEL"
     script "../main.nf"
     process "XENIUMRANGER_RELABEL"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -11,25 +10,31 @@ nextflow_process {
     tag "xeniumranger/relabel"
     tag "unzip"
 
+
     setup {
-            run("UNZIP") {
-                script "modules/nf-core/unzip/main.nf"
-                process {
-                    """
-                    input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)]
-                    """
-                }
+
+        run("UNZIP") {
+            script "modules/nf-core/unzip/main.nf"
+            process {
+                """
+                input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip', checkIfExists: true)]
+                """
             }
+        }
     }
 
     test("xeniumranger relabel") {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_relabel"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
+                input[0] = UNZIP.out.unzipped_archive
+                    .map { _, bundle ->
+                        [
+                            [id: "test_xeniumranger_relabel"],
+                            bundle,
+                            bundle + "/gene_panel.json"
+                        ]
+                    }
                 """
             }
         }
@@ -37,37 +42,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert process.out.outs != null },
-                {
-                    assert snapshot(
-                        process.out.versions,
-                        process.out.outs.get(0).get(1).findAll { file(it).name !in [
-                            "analysis.zarr.zip",
-                            "experiment.xenium",
-                            "transcripts.zarr.zip",
-                            "analysis_summary.html",
-                            "cell_feature_matrix.zarr.zip",
-                            "differential_expression.csv",
-                            "components.csv",
-                            "projection.csv",
-                            "variance.csv",
-                            "metrics_summary.csv",
-                            "clusters.csv"
-                        ]}
-                    ).match()
-                },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.zarr.zip' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'differential_expression.csv' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'components.csv' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'projection.csv' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() },
-            )
+                { assert file(process.out.outs.get(0).get(1)).isDirectory() },
+                { assert file(process.out.outs.get(0).get(1)).list().size() > 0 },
+                { assert snapshot(process.out.versions_xeniumranger).match()},
+                )
         }
     }
 
@@ -76,10 +54,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_relabel"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
+                input[0] = UNZIP.out.unzipped_archive
+                    .map { _, bundle ->
+                        [
+                            [id: "test_xeniumranger_relabel"],
+                            bundle,
+                            bundle + "/gene_panel.json"
+                        ]
+                    }
                 """
             }
         }
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap
index 7c70cfc28faa..63af4ff31a16 100644
--- a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap
+++ b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap
@@ -2,33 +2,18 @@
     "xeniumranger relabel": {
         "content": [
             [
-                "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354"
-            ],
-            [
-                "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4",
-                "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00",
-                "cell_boundaries.csv.gz:md5,8b4f2aa455a6fb14b2669a42db32ea7e",
-                "cell_boundaries.parquet:md5,e55d6a7fbec336103994baad8c8e4a9a",
-                "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6",
-                "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582",
-                "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e",
-                "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1",
-                "cells.csv.gz:md5,3cef2d7cc8cfba1d47bdb7c65c3d5d5f",
-                "cells.parquet:md5,9b30b35ab961d2d243a1426e8dc980fe",
-                "cells.zarr.zip:md5,556e47d5b14150239b10b2f801defa2b",
-                "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
-                "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98",
-                "nucleus_boundaries.csv.gz:md5,e417b6e293298870956d42c7106cbd0c",
-                "nucleus_boundaries.parquet:md5,bacbfc3c2e956d899e1d8ccba5dd7c5e",
-                "transcripts.parquet:md5,c0f40d5c61b87404bc9efb84ff0563a8"
+                [
+                    "XENIUMRANGER_RELABEL",
+                    "xeniumranger",
+                    "4.0.1.1"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-10-29T21:06:09.082129"
+        "timestamp": "2025-12-10T20:00:59.571728235"
     },
     "xeniumranger relabel stub": {
         "content": [
@@ -38,29 +23,41 @@
                         {
                             "id": "test_xeniumranger_relabel"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354"
+                    [
+                        "XENIUMRANGER_RELABEL",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ],
                 "outs": [
                     [
                         {
                             "id": "test_xeniumranger_relabel"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354"
+                "versions_xeniumranger": [
+                    [
+                        "XENIUMRANGER_RELABEL",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-10-22T15:22:34.353444"
+        "timestamp": "2025-12-10T20:01:06.673047685"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/xeniumranger/relabel/tests/nextflow.config b/modules/nf-core/xeniumranger/relabel/tests/nextflow.config
deleted file mode 100644
index e69de29bb2d1..000000000000
diff --git a/modules/nf-core/xeniumranger/rename/main.nf b/modules/nf-core/xeniumranger/rename/main.nf
index d273caf3276c..dc653daed371 100644
--- a/modules/nf-core/xeniumranger/rename/main.nf
+++ b/modules/nf-core/xeniumranger/rename/main.nf
@@ -2,31 +2,33 @@ process XENIUMRANGER_RENAME {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/xeniumranger:3.0.1"
+    container "nf-core/xeniumranger:4.0"
 
     input:
-    tuple val(meta), path(xenium_bundle)
-    val(region_name)
-    val(cassette_name)
+    tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), val(region_name), val(cassette_name)
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
-    path "versions.yml", emit: versions
+    tuple val(meta), path("${prefix}"), emit: outs
+    tuple val("${task.process}"), val("xeniumranger"), eval("xeniumranger -V | sed -e 's/.*xenium-//'"), emit: versions_xeniumranger, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "XENIUMRANGER_RENAME module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def args = task.ext.args ?: ""
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     """
+    rm -rf "${prefix}"
+
     xeniumranger rename \\
-        --id="${prefix}" \\
+        --id="XENIUMRANGER_RENAME" \\
         --xenium-bundle="${xenium_bundle}" \\
         --region-name="${region_name}" \\
         --cassette-name="${cassette_name}" \\
@@ -34,25 +36,15 @@ process XENIUMRANGER_RENAME {
         --localmem=${task.memory.toGiga()} \\
         ${args}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    mv XENIUMRANGER_RENAME/outs "${prefix}"
     """
 
     stub:
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "XENIUMRANGER_RENAME module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    mkdir -p "${prefix}/outs/"
-    touch "${prefix}/outs/fake_file.txt"
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p "${prefix}"
+    touch "${prefix}/experiment.xenium"
     """
 }
diff --git a/modules/nf-core/xeniumranger/rename/meta.yml b/modules/nf-core/xeniumranger/rename/meta.yml
index 30b79d922fe5..b3880f4ec268 100644
--- a/modules/nf-core/xeniumranger/rename/meta.yml
+++ b/modules/nf-core/xeniumranger/rename/meta.yml
@@ -1,7 +1,7 @@
 name: xeniumranger_rename
-description: The xeniumranger rename module allows you to change the sample region_name
-  and cassette_name throughout all the Xenium Onboard Analysis output files that contain
-  this information.
+description: The xeniumranger rename module allows you to change the sample
+  region_name and cassette_name throughout all the Xenium Onboard Analysis
+  output files that contain this information.
 keywords:
   - spatial
   - rename
@@ -24,36 +24,48 @@ input:
         description: Groovy Map containing sample information e.g. [ id:'test' ]
     - xenium_bundle:
         type: directory
-        description: Path to the xenium output bundle generated by the Xenium Onboard
-          Analysis pipeline
-  - region_name:
-      type: string
-      description: New region name
-  - cassette_name:
-      type: string
-      description: New cassette name
+        description: Path to the xenium output bundle generated by the Xenium
+          Onboard Analysis pipeline
+    - region_name:
+        type: string
+        description: New region name
+    - cassette_name:
+        type: string
+        description: New cassette name
 output:
   outs:
     - - meta:
-          type: file
-          description: Files containing the outputs of Cell Ranger, see official 10X
-            Genomics documentation for a complete list
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
-      - "**/outs/**":
-          type: file
-          description: Files containing the outputs of xenium ranger, see official 10X
-            Genomics documentation for a complete list of outputs
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
+          type: map
+          description: Groovy Map containing sample information e.g. [ id:'test' ]
+      - "${prefix}":
+          type: directory
+          description: Directory containing the output xenium bundle of Xenium
+            Ranger
+          pattern: "${prefix}"
+  versions_xeniumranger:
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/.*xenium-//'":
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/.*xenium-//'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@khersameesh24"
+  - "@dongzehe"
 maintainers:
   - "@khersameesh24"
+  - "@dongzehe"
diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test b/modules/nf-core/xeniumranger/rename/tests/main.nf.test
index 36bf00d95d30..07b1eaeb8b20 100644
--- a/modules/nf-core/xeniumranger/rename/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/rename/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process XENIUMRANGER_RENAME"
     script "../main.nf"
     process "XENIUMRANGER_RENAME"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -16,7 +15,7 @@ nextflow_process {
                 script "modules/nf-core/unzip/main.nf"
                 process {
                     """
-                    input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)]
+                    input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip', checkIfExists: true)]
                     """
                 }
             }
@@ -26,11 +25,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = UNZIP.out.unzipped_archive
+                    .map { _, bundle ->
+                        [
                             [id: "test_xeniumranger_rename"],
-                        ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = "test_region"
-                input[2] = "test_cassette"
+                            bundle,
+                            "test_region",
+                            "test_cassette"
+                        ]
+                    }
                 """
             }
         }
@@ -38,18 +41,16 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert process.out.outs != null },
-                {
-                    assert snapshot(
-                        process.out.versions,
-                        process.out.outs.get(0).get(1).findAll { file(it).name !in [
-                            'analysis_summary.html',
-                            'experiment.xenium',
-                        ]}
-                    ).match()
-                },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() }
+                { assert file(process.out.outs.get(0).get(1)).isDirectory() },
+                { assert file(process.out.outs.get(0).get(1) + "/analysis_summary.html").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cells.csv.gz").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cells.parquet").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cells.zarr.zip").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/transcripts.parquet").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/transcripts.zarr.zip").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/analysis.zarr.zip").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cell_feature_matrix.zarr.zip").exists() },
+                { assert snapshot(process.out.versions_xeniumranger).match()},
             )
         }
     }
@@ -59,11 +60,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = UNZIP.out.unzipped_archive
+                    .map { meta, bundle ->
+                        [
                             [id: "test_xeniumranger_rename"],
-                        ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = "test_region"
-                input[2] = "test_cassette"
+                            bundle,
+                            "test_region",
+                            "test_cassette"
+                        ]
+                    }
                 """
             }
         }
diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap
index ea57ab7e0fd6..5127d1cc25ff 100644
--- a/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap
+++ b/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap
@@ -1,4 +1,20 @@
 {
+    "xeniumranger rename": {
+        "content": [
+            [
+                [
+                    "XENIUMRANGER_RENAME",
+                    "xeniumranger",
+                    "4.0.1.1"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-10T20:01:21.033622706"
+    },
     "xeniumranger rename stub": {
         "content": [
             {
@@ -7,59 +23,41 @@
                         {
                             "id": "test_xeniumranger_rename"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,823917e7bc8f27cf314ef477fe7369eb"
+                    [
+                        "XENIUMRANGER_RENAME",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ],
                 "outs": [
                     [
                         {
                             "id": "test_xeniumranger_rename"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,823917e7bc8f27cf314ef477fe7369eb"
+                "versions_xeniumranger": [
+                    [
+                        "XENIUMRANGER_RENAME",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-30T23:10:43.918492"
-    },
-    "xeniumranger rename": {
-        "content": [
-            [
-                "versions.yml:md5,823917e7bc8f27cf314ef477fe7369eb"
-            ],
-            [
-                "analysis.zarr.zip:md5,1ffb1b86586fe6c80ce1676b79137785",
-                "cell_boundaries.csv.gz:md5,8b4f2aa455a6fb14b2669a42db32ea7e",
-                "cell_boundaries.parquet:md5,e55d6a7fbec336103994baad8c8e4a9a",
-                "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6",
-                "cell_feature_matrix.zarr.zip:md5,36f45a290cf4ee1232f2d1cd0fdbd820",
-                "cells.csv.gz:md5,3cef2d7cc8cfba1d47bdb7c65c3d5d5f",
-                "cells.parquet:md5,e1450c7eca3d7ce0d4911c95042b1303",
-                "cells.zarr.zip:md5,556e47d5b14150239b10b2f801defa2b",
-                "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "metrics_summary.csv:md5,54ad3944eb3ba6a4d7bda01bc2a6bb1c",
-                "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
-                "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98",
-                "nucleus_boundaries.csv.gz:md5,e417b6e293298870956d42c7106cbd0c",
-                "nucleus_boundaries.parquet:md5,bacbfc3c2e956d899e1d8ccba5dd7c5e",
-                "transcripts.parquet:md5,203cb05ee7689805cc505ebda9557551",
-                "transcripts.zarr.zip:md5,807e63a2ef8340e085cd899507f45395"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-10-30T23:10:34.499597"
+        "timestamp": "2025-12-10T20:01:28.086802143"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/xeniumranger/rename/tests/nextflow.config b/modules/nf-core/xeniumranger/rename/tests/nextflow.config
deleted file mode 100644
index e69de29bb2d1..000000000000
diff --git a/modules/nf-core/xeniumranger/resegment/main.nf b/modules/nf-core/xeniumranger/resegment/main.nf
index 5d28fa698a76..d52eba0e9e83 100644
--- a/modules/nf-core/xeniumranger/resegment/main.nf
+++ b/modules/nf-core/xeniumranger/resegment/main.nf
@@ -2,69 +2,44 @@ process XENIUMRANGER_RESEGMENT {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/xeniumranger:3.0.1"
+    container "nf-core/xeniumranger:4.0"
 
     input:
-    tuple val(meta), path(xenium_bundle)
-    val(expansion_distance)
-    val(dapi_filter)
-    val(boundary_stain)
-    val(interior_stain)
+    tuple val(meta), path(xenium_bundle, stageAs: "bundle/")
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
-    path "versions.yml", emit: versions
+    tuple val(meta), path("${prefix}"), emit: outs
+    tuple val("${task.process}"), val("xeniumranger"), eval("xeniumranger -V | sed -e 's/.*xenium-//'"), emit: versions_xeniumranger, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "XENIUMRANGER_RESEGMENT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ""
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    def expansion_distance = expansion_distance ? "--expansion-distance=\"${expansion_distance}\"": ""
-    def dapi_filter = dapi_filter ? "--dapi-filter=\"${dapi_filter}\"": ""
 
-    // Do not use boundary stain in analysis, but keep default interior stain and DAPI
-    def boundary_stain = boundary_stain ? "--boundary-stain=disable": ""
-    // Do not use interior stain in analysis, but keep default boundary stain and DAPI
-    def interior_stain = interior_stain ? "--interior-stain=disable": ""
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
 
     """
     xeniumranger resegment \\
-        --id="${prefix}" \\
+        --id="XENIUMRANGER_RESEGMENT" \\
         --xenium-bundle="${xenium_bundle}" \\
-        ${expansion_distance} \\
-        ${dapi_filter} \\
-        ${boundary_stain} \\
-        ${interior_stain} \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         ${args}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    rm -rf "${prefix}"
+    mv XENIUMRANGER_RESEGMENT/outs "${prefix}"
     """
 
     stub:
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "XENIUMRANGER_RESEGMENT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir -p "${prefix}/outs/"
-    touch "${prefix}/outs/fake_file.txt"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
+    mkdir -p "${prefix}"
+    touch "${prefix}/experiment.xenium"
     """
 }
diff --git a/modules/nf-core/xeniumranger/resegment/meta.yml b/modules/nf-core/xeniumranger/resegment/meta.yml
index 6666134916a8..687c67231830 100644
--- a/modules/nf-core/xeniumranger/resegment/meta.yml
+++ b/modules/nf-core/xeniumranger/resegment/meta.yml
@@ -1,7 +1,7 @@
 name: xeniumranger_resegment
-description: The xeniumranger resegment module allows you to generate a new segmentation
-  of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation
-  algorithms with modified parameters.
+description: The xeniumranger resegment module allows you to generate a new
+  segmentation of the morphology image space by rerunning the Xenium Onboard
+  Analysis (XOA) segmentation algorithms with modified parameters.
 keywords:
   - spatial
   - resegment
@@ -26,47 +26,44 @@ input:
           e.g. [ id:'xenium_experiment' ]
     - xenium_bundle:
         type: directory
-        description: Path to the xenium output bundle generated by the Xenium Onboard
-          Analysis pipeline
-  - expansion_distance:
-      type: integer
-      description: Nuclei boundary expansion distance in µm. Only for use when nucleus
-        segmentation provided as input. Default-5 (accepted range 0 - 100)
-  - dapi_filter:
-      type: integer
-      description: Minimum intensity in photoelectrons to filter nuclei default-100
-        range of values is 0 to 99th percentile of image stack or 1000, whichever is
-        larger
-  - boundary_stain:
-      type: string
-      description: Specify the name of the boundary stain to use or disable possible
-        options are default-ATP1A1/CD45/E-Cadherin or disable
-  - interior_stain:
-      type: string
-      description: Specify the name of the interior stain to use or disable possible
-        options are default-18S or disable
+        description: Path to the xenium output bundle generated by the Xenium
+          Onboard Analysis pipeline
 output:
   outs:
     - - meta:
-          type: file
-          description: Files containing the outputs of Cell Ranger, see official 10X
-            Genomics documentation for a complete list
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
-      - "**/outs/**":
-          type: file
-          description: Files containing the outputs of xenium ranger, see official 10X
-            Genomics documentation for a complete list of outputs
-          pattern: "${meta.id}/outs/*"
-          ontologies: []
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "${prefix}":
+          type: directory
+          description: Directory containing the output xenium bundle of Xenium
+            Ranger
+          pattern: "${prefix}"
+  versions_xeniumranger:
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/.*xenium-//'":
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/.*xenium-//'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@khersameesh24"
+  - "@dongzehe"
 maintainers:
   - "@khersameesh24"
+  - "@dongzehe"
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
index 85fc63e580c2..c24d897d72e2 100644
--- a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
+++ b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process XENIUMRANGER_RESEGMENT"
     script "../main.nf"
     process "XENIUMRANGER_RESEGMENT"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -12,42 +11,45 @@ nextflow_process {
     tag "unzip"
 
     setup {
-            run("UNZIP") {
-                script "modules/nf-core/unzip/main.nf"
-                process {
-                    """
-                    input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)]
-                    """
-                }
+        run("UNZIP") {
+            script "modules/nf-core/unzip/main.nf"
+            process {
+                """
+                input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip', checkIfExists: true)]
+                """
             }
+        }
     }
 
     test("xeniumranger resegment") {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_resegment"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
+                input[0] = UNZIP.out.unzipped_archive.map {
+                    _, bundle ->
+                        [
+                            [id: "test_xeniumranger_resegment"],
+                            bundle
+                        ]
+                }
                 """
             }
         }
         then {
+            // xeniumranger doesn't generate deterministic outputs, so we can't use snapshot
             assertAll(
                 { assert process.success },
                 { assert process.out.outs != null },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.csv.gz' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.parquet' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.zarr.zip' }).exists() },
-                { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() },
-                { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() }
+                { assert file(process.out.outs.get(0).get(1)).isDirectory() },
+                { assert file(process.out.outs.get(0).get(1) + "/analysis_summary.html").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cells.csv.gz").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cells.parquet").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cells.zarr.zip").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/transcripts.parquet").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/transcripts.zarr.zip").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/analysis.zarr.zip").exists() },
+                { assert file(process.out.outs.get(0).get(1) + "/cell_feature_matrix.zarr.zip").exists()},
+                { assert snapshot(process.out.versions_xeniumranger).match()},
             )
         }
     }
@@ -57,13 +59,13 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                        [id: "test_xeniumranger_resegment"],
-                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
+                input[0] = UNZIP.out.unzipped_archive.map {
+                    _, bundle ->
+                        [
+                            [id: "test_xeniumranger_resegment"],
+                            bundle
+                        ]
+                }
                 """
             }
         }
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap
index 16f94c14ebf2..cbeaa885f6dd 100644
--- a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap
+++ b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap
@@ -1,4 +1,20 @@
 {
+    "xeniumranger resegment": {
+        "content": [
+            [
+                [
+                    "XENIUMRANGER_RESEGMENT",
+                    "xeniumranger",
+                    "4.0.1.1"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-10T21:21:39.73207635"
+    },
     "xeniumranger resegment stub": {
         "content": [
             {
@@ -7,29 +23,41 @@
                         {
                             "id": "test_xeniumranger_resegment"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4671141281357e0ce26d9cb35fed23a8"
+                    [
+                        "XENIUMRANGER_RESEGMENT",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ],
                 "outs": [
                     [
                         {
                             "id": "test_xeniumranger_resegment"
                         },
-                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,4671141281357e0ce26d9cb35fed23a8"
+                "versions_xeniumranger": [
+                    [
+                        "XENIUMRANGER_RESEGMENT",
+                        "xeniumranger",
+                        "4.0.1.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-10-30T23:22:35.438329"
+        "timestamp": "2025-12-10T21:21:47.102042217"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/xeniumranger/resegment/tests/nextflow.config b/modules/nf-core/xeniumranger/resegment/tests/nextflow.config
deleted file mode 100644
index e69de29bb2d1..000000000000