diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 12d201a5d51..7b6737e0cfe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -662,6 +662,15 @@ jobs:
             path: subworkflows/nf-core/fastq_align_bwa
           - profile: conda
             path: subworkflows/nf-core/fasta_newick_epang_gappa
+          - profile: conda
+            path: modules/nf-core/xeniumranger/relabel
+          - profile: conda
+            path: modules/nf-core/xeniumranger/rename
+          - profile: conda
+            path: modules/nf-core/xeniumranger/resegment
+          - profile: conda
+            path: modules/nf-core/xeniumranger/import-segmentation
+
     env:
       NXF_ANSI_LOG: false
       NFTEST_VER: "0.9.0"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 351a51a9b3a..1e4ceb6a30c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:
diff --git a/modules/nf-core/xeniumranger/.gitignore b/modules/nf-core/xeniumranger/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/modules/nf-core/xeniumranger/Dockerfile b/modules/nf-core/xeniumranger/Dockerfile
new file mode 100644
index 00000000000..daa3c965c5e
--- /dev/null
+++ b/modules/nf-core/xeniumranger/Dockerfile
@@ -0,0 +1,29 @@
+#  Use a base image with the required operating system
+FROM ubuntu:20.04 AS builder
+
+LABEL authors="Sameesh Kher <sameesh.kher@dkfz-heidelberg.de>" \
+    description="Docker image containing Xenium Ranger"
+
+RUN apt-get update --allow-releaseinfo-change \
+    && apt-get install -y \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+# 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
+
+# install xenium ranger
+RUN tar -xzvf /xeniumranger-3.0.1.tar.gz && \
+    rm /xeniumranger-3.0.1.tar.gz
+
+# Set environment variables
+# ENV PATH="xeniumranger-xenium3.0/bin:$PATH"
+
+# multistage to reduce image size
+FROM ubuntu:20.04
+
+# Set environment variables
+ENV PATH="/xeniumranger-xenium3.0/bin:$PATH"
+
+# copy over xenium from builder
+COPY --from=builder /xeniumranger-xenium3.0 /xeniumranger-xenium3.0/
diff --git a/modules/nf-core/xeniumranger/README.md b/modules/nf-core/xeniumranger/README.md
new file mode 100644
index 00000000000..9bbe56b01c2
--- /dev/null
+++ b/modules/nf-core/xeniumranger/README.md
@@ -0,0 +1,20 @@
+# Updating the docker container and making a new module release
+
+Xenium Ranger is a commercial tool from 10X Genomics. The container provided for the xeniumranger nf-core module is not provided nor supported by 10x Genomics. Updating the Xenium Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
+
+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)
+
+3. Create and test the container:
+
+```bash
+docker build . -t quay.io/nf-core/xeniumranger:<VERSION>
+```
+
+4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
+
+```bash
+docker push quay.io/nf-core/xeniumranger:<VERSION>
+```
diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf
new file mode 100644
index 00000000000..50b17272a16
--- /dev/null
+++ b/modules/nf-core/xeniumranger/import-segmentation/main.nf
@@ -0,0 +1,81 @@
+process XENIUMRANGER_IMPORT_SEGMENTATION {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "nf-core/xeniumranger:3.0.1"
+
+    input:
+    tuple val(meta), path(xenium_bundle)
+    val(expansion_distance)
+    path(coordinate_transform)
+    path(nuclei)
+    path(cells)
+    path(transcript_assignment)
+    path(viz_polygons)
+
+    output:
+    tuple val(meta), path("**/outs/**"), emit: outs
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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}\"": ""
+
+    def nuclei_detection = nuclei ? "--nuclei=\"${nuclei}\"": ""
+    def cells = cells ? "--cells=\"${cells}\"": ""
+
+    // transcript based segmentation
+    def transcript_assignment = transcript_assignment ? "--transcript-assignment=\"${transcript_assignment}\"": ""
+    def viz_polygons = viz_polygons ? "--viz-polygons=\"${viz_polygons}\"":""
+
+    // shared argument
+    def units = coordinate_transform ? "--units=microns": "--units=pixels"
+
+    """
+    xeniumranger import-segmentation \\
+        --id="${prefix}" \\
+        --xenium-bundle="${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
+    """
+
+    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 ?: "${meta.id}"
+    """
+    mkdir -p "${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
+    """
+}
diff --git a/modules/nf-core/xeniumranger/import-segmentation/meta.yml b/modules/nf-core/xeniumranger/import-segmentation/meta.yml
new file mode 100644
index 00000000000..c3a34ec5339
--- /dev/null
+++ b/modules/nf-core/xeniumranger/import-segmentation/meta.yml
@@ -0,0 +1,84 @@
+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.
+keywords:
+  - spatial
+  - segmentation
+  - import segmentation
+  - nuclear segmentation
+  - cell segmentation
+  - xeniumranger
+  - imaging
+tools:
+  - xeniumranger:
+      description: |
+        Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
+      homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest"
+      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"
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing run information
+          e.g. [id:'xenium_bundle_path']
+    - 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
+  - - 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.
+  - - 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.
+  - - transcript_assignment:
+        type: file
+        description: |
+          Transcript CSV with cell assignment from Baysor v0.6. Error if --cells or --nuclei arguments are used.
+  - - 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.
+output:
+  - outs:
+      - meta:
+          type: file
+          description: Files containing the outputs of Cell Ranger, see official 10X Genomics
+            documentation for a complete list
+          pattern: "${meta.id}/outs/*"
+      - "**/outs/**":
+          type: file
+          description: Files containing the outputs of xenium ranger, see official 10X
+            Genomics documentation for a complete list of outputs
+          pattern: "${meta.id}/outs/*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
new file mode 100644
index 00000000000..54d3ba00209
--- /dev/null
+++ b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
@@ -0,0 +1,314 @@
+nextflow_process {
+
+    name "Test Process XENIUMRANGER_IMPORT_SEGMENTATION"
+    script "../main.nf"
+    process "XENIUMRANGER_IMPORT_SEGMENTATION"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "xeniumranger"
+    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 {
+            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 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") {
+        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"
+                """
+            }
+        }
+        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() },
+            )
+        }
+    }
+
+    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] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..1c312ae0f3b
--- /dev/null
+++ b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap
@@ -0,0 +1,127 @@
+{
+    "xeniumranger import-segmentation": {
+        "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"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T23:22:58.158857"
+    },
+    "xeniumranger import-segmentation stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_xeniumranger_import-segmentation"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
+                ],
+                "outs": [
+                    [
+                        {
+                            "id": "test_xeniumranger_import-segmentation"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63"
+                ]
+            }
+        ],
+        "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"
+        },
+        "timestamp": "2024-10-29T23:11:37.18721"
+    }
+}
\ 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
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/tags.yml b/modules/nf-core/xeniumranger/import-segmentation/tests/tags.yml
new file mode 100644
index 00000000000..90c2b80563c
--- /dev/null
+++ b/modules/nf-core/xeniumranger/import-segmentation/tests/tags.yml
@@ -0,0 +1,2 @@
+xeniumranger/import-segmentation:
+  - "modules/nf-core/xeniumranger/import-segmentation/**"
diff --git a/modules/nf-core/xeniumranger/relabel/main.nf b/modules/nf-core/xeniumranger/relabel/main.nf
new file mode 100644
index 00000000000..b06fe9ea13e
--- /dev/null
+++ b/modules/nf-core/xeniumranger/relabel/main.nf
@@ -0,0 +1,56 @@
+process XENIUMRANGER_RELABEL {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "nf-core/xeniumranger:3.0.1"
+
+    input:
+    tuple val(meta), path(xenium_bundle)
+    path(gene_panel)
+
+    output:
+    tuple val(meta), path("**/outs/**"), emit: outs
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "XENIUMRANGER_RELABEL module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    xeniumranger relabel \\
+        --id="${prefix}" \\
+        --xenium-bundle="${xenium_bundle}" \\
+        --panel="${gene_panel}" \\
+        --localcores=${task.cpus} \\
+        --localmem=${task.memory.toGiga()} \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
+    END_VERSIONS
+    """
+
+    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 "${prefix}/outs/fake_file.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/xeniumranger/relabel/meta.yml b/modules/nf-core/xeniumranger/relabel/meta.yml
new file mode 100644
index 00000000000..85c1dbfa3a1
--- /dev/null
+++ b/modules/nf-core/xeniumranger/relabel/meta.yml
@@ -0,0 +1,53 @@
+name: xeniumranger_relabel
+description: The xeniumranger relabel module allows you to change the gene labels
+  applied to decoded transcripts.
+keywords:
+  - spatial
+  - relabel
+  - gene labels
+  - transcripts
+  - xeniumranger
+tools:
+  - xeniumranger:
+      description: |
+        Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
+      homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest"
+      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
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing run information
+          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
+output:
+  - outs:
+      - meta:
+          type: file
+          description: Files containing the outputs of Cell Ranger, see official 10X Genomics
+            documentation for a complete list
+          pattern: "${meta.id}/outs/*"
+      - "**/outs/**":
+          type: file
+          description: Files containing the outputs of xenium ranger, see official 10X
+            Genomics documentation for a complete list of outputs
+          pattern: "${meta.id}/outs/*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
new file mode 100644
index 00000000000..d09627386c3
--- /dev/null
+++ b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
@@ -0,0 +1,93 @@
+nextflow_process {
+
+    name "Test Process XENIUMRANGER_RELABEL"
+    script "../main.nf"
+    process "XENIUMRANGER_RELABEL"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "xeniumranger"
+    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)]
+                    """
+                }
+            }
+    }
+
+    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"
+                """
+            }
+        }
+        then {
+            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() },
+            )
+        }
+    }
+
+    test("xeniumranger relabel stub") {
+        options "-stub"
+        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"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap
new file mode 100644
index 00000000000..7c70cfc28fa
--- /dev/null
+++ b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap
@@ -0,0 +1,66 @@
+{
+    "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"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T21:06:09.082129"
+    },
+    "xeniumranger relabel stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_xeniumranger_relabel"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354"
+                ],
+                "outs": [
+                    [
+                        {
+                            "id": "test_xeniumranger_relabel"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-22T15:22:34.353444"
+    }
+}
\ 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
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/modules/nf-core/xeniumranger/relabel/tests/tags.yml b/modules/nf-core/xeniumranger/relabel/tests/tags.yml
new file mode 100644
index 00000000000..1cb37a80de0
--- /dev/null
+++ b/modules/nf-core/xeniumranger/relabel/tests/tags.yml
@@ -0,0 +1,2 @@
+xeniumranger/relabel:
+  - "modules/nf-core/xeniumranger/relabel/**"
diff --git a/modules/nf-core/xeniumranger/rename/main.nf b/modules/nf-core/xeniumranger/rename/main.nf
new file mode 100644
index 00000000000..d273caf3276
--- /dev/null
+++ b/modules/nf-core/xeniumranger/rename/main.nf
@@ -0,0 +1,58 @@
+process XENIUMRANGER_RENAME {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "nf-core/xeniumranger:3.0.1"
+
+    input:
+    tuple val(meta), path(xenium_bundle)
+    val(region_name)
+    val(cassette_name)
+
+    output:
+    tuple val(meta), path("**/outs/**"), emit: outs
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "XENIUMRANGER_RENAME module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    xeniumranger rename \\
+        --id="${prefix}" \\
+        --xenium-bundle="${xenium_bundle}" \\
+        --region-name="${region_name}" \\
+        --cassette-name="${cassette_name}" \\
+        --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
+    """
+
+    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
+    """
+}
diff --git a/modules/nf-core/xeniumranger/rename/meta.yml b/modules/nf-core/xeniumranger/rename/meta.yml
new file mode 100644
index 00000000000..d7842b007a7
--- /dev/null
+++ b/modules/nf-core/xeniumranger/rename/meta.yml
@@ -0,0 +1,55 @@
+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.
+keywords:
+  - spatial
+  - rename
+  - gene labels
+  - transcripts
+  - xeniumranger
+tools:
+  - xeniumranger:
+      description: |
+        Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
+      homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest"
+      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"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        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
+output:
+  - outs:
+      - meta:
+          type: file
+          description: Files containing the outputs of Cell Ranger, see official 10X Genomics
+            documentation for a complete list
+          pattern: "${meta.id}/outs/*"
+      - "**/outs/**":
+          type: file
+          description: Files containing the outputs of xenium ranger, see official 10X
+            Genomics documentation for a complete list of outputs
+          pattern: "${meta.id}/outs/*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test b/modules/nf-core/xeniumranger/rename/tests/main.nf.test
new file mode 100644
index 00000000000..3819a310d19
--- /dev/null
+++ b/modules/nf-core/xeniumranger/rename/tests/main.nf.test
@@ -0,0 +1,77 @@
+nextflow_process {
+
+    name "Test Process XENIUMRANGER_RENAME"
+    script "../main.nf"
+    process "XENIUMRANGER_RENAME"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "xeniumranger"
+    tag "xeniumranger/rename"
+    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 rename") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                            [id: "test_xeniumranger_rename"],
+                        ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = "test_region"
+                input[2] = "test_cassette"
+                """
+            }
+        }
+        then {
+            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() }
+            )
+        }
+    }
+
+    test("xeniumranger rename stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                            [id: "test_xeniumranger_rename"],
+                        ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = "test_region"
+                input[2] = "test_cassette"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap
new file mode 100644
index 00000000000..ea57ab7e0fd
--- /dev/null
+++ b/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap
@@ -0,0 +1,65 @@
+{
+    "xeniumranger rename stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_xeniumranger_rename"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,823917e7bc8f27cf314ef477fe7369eb"
+                ],
+                "outs": [
+                    [
+                        {
+                            "id": "test_xeniumranger_rename"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,823917e7bc8f27cf314ef477fe7369eb"
+                ]
+            }
+        ],
+        "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"
+        },
+        "timestamp": "2024-10-30T23:10:34.499597"
+    }
+}
\ 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
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/modules/nf-core/xeniumranger/rename/tests/tags.yml b/modules/nf-core/xeniumranger/rename/tests/tags.yml
new file mode 100644
index 00000000000..1f9026ac618
--- /dev/null
+++ b/modules/nf-core/xeniumranger/rename/tests/tags.yml
@@ -0,0 +1,2 @@
+xeniumranger/rename:
+  - "modules/nf-core/xeniumranger/rename/**"
diff --git a/modules/nf-core/xeniumranger/resegment/main.nf b/modules/nf-core/xeniumranger/resegment/main.nf
new file mode 100644
index 00000000000..5d28fa698a7
--- /dev/null
+++ b/modules/nf-core/xeniumranger/resegment/main.nf
@@ -0,0 +1,70 @@
+process XENIUMRANGER_RESEGMENT {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "nf-core/xeniumranger:3.0.1"
+
+    input:
+    tuple val(meta), path(xenium_bundle)
+    val(expansion_distance)
+    val(dapi_filter)
+    val(boundary_stain)
+    val(interior_stain)
+
+    output:
+    tuple val(meta), path("**/outs/**"), emit: outs
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "XENIUMRANGER_RESEGMENT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ""
+    def prefix = task.ext.prefix ?: "${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": ""
+
+    """
+    xeniumranger resegment \\
+        --id="${prefix}" \\
+        --xenium-bundle="${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
+    """
+
+    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 ?: "${meta.id}"
+    """
+    mkdir -p "${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
+    """
+}
diff --git a/modules/nf-core/xeniumranger/resegment/meta.yml b/modules/nf-core/xeniumranger/resegment/meta.yml
new file mode 100644
index 00000000000..af0e88826b0
--- /dev/null
+++ b/modules/nf-core/xeniumranger/resegment/meta.yml
@@ -0,0 +1,58 @@
+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.
+keywords:
+  - spatial
+  - resegment
+  - morphology
+  - segmentation
+  - xeniumranger
+tools:
+  - xeniumranger:
+      description: |
+        Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
+      homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest"
+      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"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing run information
+          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
+output:
+  - outs:
+      - meta:
+          type: file
+          description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
+          pattern: "${meta.id}/outs/*"
+      - "**/outs/**":
+          type: file
+          description: Files containing the outputs of xenium ranger, see official 10X Genomics documentation for a complete list of outputs
+          pattern: "${meta.id}/outs/*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
new file mode 100644
index 00000000000..861c2414565
--- /dev/null
+++ b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
@@ -0,0 +1,77 @@
+nextflow_process {
+
+    name "Test Process XENIUMRANGER_RESEGMENT"
+    script "../main.nf"
+    process "XENIUMRANGER_RESEGMENT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "xeniumranger"
+    tag "xeniumranger/resegment"
+    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 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] = []
+                """
+            }
+        }
+        then {
+            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() }
+            )
+        }
+    }
+
+    test("xeniumranger resegment stub") {
+        options "-stub"
+        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] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap
new file mode 100644
index 00000000000..16f94c14ebf
--- /dev/null
+++ b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "xeniumranger resegment stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_xeniumranger_resegment"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4671141281357e0ce26d9cb35fed23a8"
+                ],
+                "outs": [
+                    [
+                        {
+                            "id": "test_xeniumranger_resegment"
+                        },
+                        "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4671141281357e0ce26d9cb35fed23a8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T23:22:35.438329"
+    }
+}
\ 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
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/modules/nf-core/xeniumranger/resegment/tests/tags.yml b/modules/nf-core/xeniumranger/resegment/tests/tags.yml
new file mode 100644
index 00000000000..99f47c82ae9
--- /dev/null
+++ b/modules/nf-core/xeniumranger/resegment/tests/tags.yml
@@ -0,0 +1,2 @@
+xeniumranger/resegment:
+  - "modules/nf-core/xeniumranger/resegment/**"