mcmero · Sep 12, 2025 · Sep 1, 2025 · Sep 3, 2025 · Sep 8, 2025 · Sep 10, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.2.0 - 2025-09-12
+
+Add segmentation report.
+
 ## v0.1.0 - 2025-08-29
 
 Initial release of WEHI-SODA-Hub/spatialproteomics, created with the [nf-core](https://nf-co.re/) template.
diff --git a/README.md b/README.md
@@ -26,6 +26,39 @@ are run separately, and then consolidated into whole cells with nuclei with full
 shape and intensity measurements per compartment. The output GeoJSON files can
 be viewed in QuPath.
 
+<details>
+  <summary>Click to view Mermaid diagram</summary>
+  ```mermaid
+  flowchart TD
+  A("COMET TIFF") --> B["Extract markers"]
+  B --> C["Background
+          subtraction"]
+  C --> D{"Segmentation
+              method"} & O["Backsub TIFF"]
+      N("COMET/MIBI TIFF") --> D
+      D -- Cellpose (COMET only) --> E["sopa convert"]
+      E  --> F["sopa patchify"]
+      F --> G["cellpose
+              (nuclear)"]
+      F --> H["cellpose
+              (whole-cell)"]
+      G --> I["sopa resolve"]
+      H --> I
+      I --> J["parquet to tiff"]
+      J --> K["Cell measurement"]
+      D -- Mesmer (COMET/MIBI) --> L["mesmer
+                                     (nuclear)"]
+      D -- Mesmer (COMET/MIBI) --> M["mesmer
+                                     (whole-cell)"]
+      L --> K
+      M --> K
+      K --> P("GeoJSON")
+      K --> Q["segmentation
+              report"]
+      Q --> R("html file"]
+  ```
+</details>
+
 ![spatialproteomics workflow](assets/spatialproteomics_workflow.png)
 
 The pipeline uses the following tools:
@@ -39,6 +72,8 @@ The pipeline uses the following tools:
   QuPath API to calculate compartment measurements and intensities.
 - [sopa](https://github.com/gustaveroussy/sopa) -- we use the sopa CLI tool to
   patchify images and perform cellpose segmentation.
+- [spatialVis](https://github.com/WEHI-SODA-Hub/spatialVis) -- R package for spatial
+  analyses, used to generate plots for the segmentation report.
 
 Please see the [docs for more detailed information on pipeline usage and output](docs/README.md)
 

diff --git a/assets/spatialproteomics_workflow.png b/assets/spatialproteomics_workflow.png
diff --git a/docs/output.md b/docs/output.md
@@ -50,6 +50,11 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   segmentations, optionally containing measurements and intensity values per
   cell, compatible with QuPath.
 
+#### Segmentation report
+
+- `segmentationreport/sample/sample.html` -- html file for visualising report.
+- `segmentationreport/sample/sample_report_template_files` -- files necessary to display report.
+
 #### Data provenance
 
 - `pipeline_info/`

diff --git a/docs/usage.md b/docs/usage.md
@@ -160,6 +160,12 @@ The following Mesmer parameters can be set:
 | pixel_size_microns          | Pixel size in microns, use 0.28 for COMET and 0.390625 for MIBI                            |
 | estimate_cell_boundary_dist | Where no matching membrane ROI exists, expand the nucleus by this many pixels              |
 
+### Report parameters
+
+| Parameter Name  | Description                         |
+| --------------- | ----------------------------------- |
+| generate_report | Generate segmentation report for QC |
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:

diff --git a/modules/local/segmentationreport/environment.yml b/modules/local/segmentationreport/environment.yml
@@ -0,0 +1,11 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-quarto=1.4.4
+  - conda-forge::r-magick=2.8.5
+  - conda-forge::r-devtools=2.4.5
+  - bioconda::bioconductor-spatialexperiment=1.16.0
+  - bioconda::bioconductor-spasim=1.8.0
diff --git a/modules/local/segmentationreport/main.nf b/modules/local/segmentationreport/main.nf
@@ -0,0 +1,87 @@
+process SEGMENTATIONREPORT {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container 'ghcr.io/wehi-soda-hub/spatialvis:0.1.4'
+
+    input:
+    tuple val(meta),
+        path(annotations),
+        val(run_mesmer),
+        val(run_cellpose),
+        val(nuclear_channel),
+        val(membrane_channels)
+
+    output:
+    tuple val(meta), path("*/*.html"), path("*/*_files/*"), emit: report
+    tuple val(meta), path("*/*.rds"), emit: rds, optional: true
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    """
+    Rscript -e "spatialVis::copy_report_template(
+        template_name = 'segmentation_report_template.qmd',
+        output_dir = '.',
+        overwrite = TRUE
+    )"
+    quarto render segmentation_report_template.qmd \\
+        --to html \\
+        --no-cache \\
+        --output ${prefix}.html \\
+        ${args} \\
+        -P sample_name:${meta.id} \\
+        -P geojson_file:${annotations} \\
+        -P nuclear_channel:${nuclear_channel} \\
+        -P membrane_channels:"${membrane_channels}" \\
+        -P run_cellpose:${run_cellpose} \\
+        -P cellpose_diameter:${params.cellpose_diameter} \\
+        -P cellpose_min_area:${params.cellpose_min_area} \\
+        -P cellpose_flow_threshold:${params.cellpose_flow_threshold} \\
+        -P cellpose_cellprob_threshold:${params.cellpose_cellprob_threshold} \\
+        -P cellpose_model_type:${params.cellpose_model_type} \\
+        -P cellpose_pretrained_model:${params.cellpose_pretrained_model} \\
+        -P run_mesmer:${run_mesmer} \\
+        -P mesmer_segmentation_level:${params.mesmer_segmentation_level} \\
+        -P mesmer_maxima_threshold:${params.mesmer_maxima_threshold} \\
+        -P mesmer_interior_threshold:${params.mesmer_interior_threshold} \\
+        -P mesmer_maxima_smooth:${params.mesmer_maxima_smooth} \\
+        -P mesmer_min_nuclei_area:${params.mesmer_min_nuclei_area} \\
+        -P mesmer_remove_border_cells:${params.mesmer_remove_border_cells} \\
+        -P mesmer_pixel_expansion:${params.mesmer_pixel_expansion} \\
+        -P mesmer_padding:${params.mesmer_padding}
+
+    mkdir -p ${prefix}
+    mv ${prefix}.html ${prefix}
+    if [[ -f ${prefix}.rds ]]; then
+        mv ${prefix}.rds ${prefix}
+    fi
+    cp -r segmentation_report_template_files ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(Rscript -e "cat(as.character(getRversion()))")
+        spatialVis: \$(Rscript -e "cat(as.character(packageVersion('spatialVis')))")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}/segmentation_report_template_files
+    touch ${prefix}/${prefix}.html
+    touch ${prefix}/${prefix}.rds
+    touch ${prefix}/segmentation_report_template_files/foo.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(Rscript -e "cat(as.character(getRversion()))")
+        spatialVis: \$(Rscript -e "cat(as.character(packageVersion('spatialVis')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/segmentationreport/tests/main.nf.test b/modules/local/segmentationreport/tests/main.nf.test
@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process SEGMENTATIONREPORT"
+    script "../main.nf"
+    process "SEGMENTATIONREPORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "segmentationreport"
+
+    test("segmentationreport - basic functionality") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file('/vast/scratch/users/cmero.ma/results/spatialproteomics_test/cellmeasurement/test.geojson'),
+                    true,
+                    false
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("segmentationreport - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'stub_test' ], // meta map
+                    file('/vast/scratch/users/cmero.ma/results/spatialproteomics_test/cellmeasurement/test.geojson'),
+                    true,
+                    false
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/segmentationreport/tests/main.nf.test.snap b/modules/local/segmentationreport/tests/main.nf.test.snap
@@ -0,0 +1,150 @@
+{
+    "segmentationreport - basic functionality": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.html:md5,978a4490880fb404e965aea8838d8f37",
+                        [
+                            [
+                                "channel_intensities-1.png:md5,6a0c625d84e7e87344c68e83bd508505",
+                                "compartment_measurements-1.png:md5,67e32361a18ca731b2b69e77c3ef3133",
+                                "unnamed-chunk-1-1.png:md5,1bc975856040cdf40996f4a9ecee2af7"
+                            ],
+                            [
+                                [
+                                    "bootstrap-bb462d781dde1847d9e3ccf7736099dd.min.css:md5,bb462d781dde1847d9e3ccf7736099dd",
+                                    "bootstrap-icons.css:md5,2318f137d201fbf51601fa0faba6bef7",
+                                    "bootstrap-icons.woff:md5,1a51dfbe5467607389d603c02a77cd10",
+                                    "bootstrap.min.js:md5,e2b09c06f0e714b6144a6788a28e3950"
+                                ],
+                                [
+                                    "clipboard.min.js:md5,15f52a1ee547f2bdd46e56747332ca2d"
+                                ],
+                                [
+                                    "anchor.min.js:md5,91bcf6cd1fd88fec3f109811e5fc3546",
+                                    "popper.min.js:md5,3a4a291ccf3f1ea0f82b641542fd3827",
+                                    "quarto-syntax-highlighting-c8ad9e5dbd60b7b70b38521ab19b7da4.css:md5,c8ad9e5dbd60b7b70b38521ab19b7da4",
+                                    "quarto.js:md5,6f4245742deb3cc92337dbe2701ccfe1",
+                                    [
+                                        "tabsets.js:md5,e8d6a8862b33ccc461f8fd532e05b365"
+                                    ],
+                                    "tippy.css:md5,ebd6f8ce46a677e1a4f5f8a8317109a9",
+                                    "tippy.umd.min.js:md5,d828775275749701b48bd9d958814111"
+                                ]
+                            ]
+                        ]
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,a36295eacb48d679e04b9d2c71e4f0eb"
+                ],
+                "rds": [
+
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.html:md5,978a4490880fb404e965aea8838d8f37",
+                        [
+                            [
+                                "channel_intensities-1.png:md5,6a0c625d84e7e87344c68e83bd508505",
+                                "compartment_measurements-1.png:md5,67e32361a18ca731b2b69e77c3ef3133",
+                                "unnamed-chunk-1-1.png:md5,1bc975856040cdf40996f4a9ecee2af7"
+                            ],
+                            [
+                                [
+                                    "bootstrap-bb462d781dde1847d9e3ccf7736099dd.min.css:md5,bb462d781dde1847d9e3ccf7736099dd",
+                                    "bootstrap-icons.css:md5,2318f137d201fbf51601fa0faba6bef7",
+                                    "bootstrap-icons.woff:md5,1a51dfbe5467607389d603c02a77cd10",
+                                    "bootstrap.min.js:md5,e2b09c06f0e714b6144a6788a28e3950"
+                                ],
+                                [
+                                    "clipboard.min.js:md5,15f52a1ee547f2bdd46e56747332ca2d"
+                                ],
+                                [
+                                    "anchor.min.js:md5,91bcf6cd1fd88fec3f109811e5fc3546",
+                                    "popper.min.js:md5,3a4a291ccf3f1ea0f82b641542fd3827",
+                                    "quarto-syntax-highlighting-c8ad9e5dbd60b7b70b38521ab19b7da4.css:md5,c8ad9e5dbd60b7b70b38521ab19b7da4",
+                                    "quarto.js:md5,6f4245742deb3cc92337dbe2701ccfe1",
+                                    [
+                                        "tabsets.js:md5,e8d6a8862b33ccc461f8fd532e05b365"
+                                    ],
+                                    "tippy.css:md5,ebd6f8ce46a677e1a4f5f8a8317109a9",
+                                    "tippy.umd.min.js:md5,d828775275749701b48bd9d958814111"
+                                ]
+                            ]
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a36295eacb48d679e04b9d2c71e4f0eb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.4"
+        },
+        "timestamp": "2025-09-01T13:49:50.280243443"
+    },
+    "segmentationreport - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "stub_test"
+                        },
+                        "stub_test.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "foo.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "stub_test"
+                        },
+                        "stub_test.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,a36295eacb48d679e04b9d2c71e4f0eb"
+                ],
+                "rds": [
+                    [
+                        {
+                            "id": "stub_test"
+                        },
+                        "stub_test.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "stub_test"
+                        },
+                        "stub_test.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "foo.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a36295eacb48d679e04b9d2c71e4f0eb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.4"
+        },
+        "timestamp": "2025-09-01T13:12:50.675902625"
+    }
+}