diff --git a/conf/modules.config b/conf/modules.config
index 1311949..76b219a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -47,15 +47,24 @@ process {
     withName: "DEEPCELL_MESMER" {
         ext.prefix = { "mask_${meta.id}" }
         ext.args = '--image-mpp=0.215 --nuclear-channel 0 --compartment nuclear'
+        ext.when = {params.segmentation && params.segmentation.split(',').contains('mesmer')}
         publishDir = [
             path: { "${params.outdir}/segmentation/deepcell_mesmer" },
             mode: params.publish_dir_mode,
         ]
     }
 
+    withName: "CELLPOSE" {
+        ext.when = {params.segmentation && params.segmentation.split(',').contains('cellpose')}
+        publishDir = [
+            path: { "${params.outdir}/segmentation/cellpose" },
+            mode: params.publish_dir_mode,
+        ]
+    }
+
     withName: MCQUANT {
         publishDir = [
-            path: { "${params.outdir}/quantification/mcquant" },
+            path: { "${params.outdir}/quantification/mcquant/${meta2.segmenter}" },
             mode: params.publish_dir_mode,
         ]
     }
diff --git a/modules.json b/modules.json
index 3a70128..3329a8f 100644
--- a/modules.json
+++ b/modules.json
@@ -25,6 +25,12 @@
                     "cellpose": {
                         "branch": "master",
                         "git_sha": "716ef3019b66772a817b417078edce2f7b337858",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cellpose/cellpose.diff"
+                    },
+                    "coreograph": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "deepcell/mesmer": {
diff --git a/modules/nf-core/cellpose/cellpose.diff b/modules/nf-core/cellpose/cellpose.diff
new file mode 100644
index 0000000..44b9c75
--- /dev/null
+++ b/modules/nf-core/cellpose/cellpose.diff
@@ -0,0 +1,15 @@
+Changes in module 'nf-core/cellpose'
+--- modules/nf-core/cellpose/main.nf
++++ modules/nf-core/cellpose/main.nf
+@@ -25,6 +25,9 @@
+     def model_command = model ? "--pretrained_model $model" : ""
+     def VERSION = '2.1.1'
+     """
++    export HOME=\$PWD
++    export NUMBA_CACHE_DIR=\$PWD
++    
+     cellpose \
+     --image_path $image \
+     --save_tif \
+
+************************************************************
diff --git a/modules/nf-core/cellpose/main.nf b/modules/nf-core/cellpose/main.nf
index a2b2206..6778e6b 100644
--- a/modules/nf-core/cellpose/main.nf
+++ b/modules/nf-core/cellpose/main.nf
@@ -25,6 +25,9 @@ process CELLPOSE {
     def model_command = model ? "--pretrained_model $model" : ""
     def VERSION = '2.1.1'
     """
+    export HOME=\$PWD
+    export NUMBA_CACHE_DIR=\$PWD
+    
     cellpose \
     --image_path $image \
     --save_tif \
diff --git a/nextflow.config b/nextflow.config
index 5a64850..2f9f598 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,6 +13,8 @@ params {
     input_sample               = null
     input_cycle                = null
     marker_sheet               = null
+    segmentation               = 'mesmer'
+    cellpose_model             = []
 
     // Illumination correction
     illumination               = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 7b24b69..c0209e5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -65,6 +65,15 @@
                     "type": "string",
                     "enum": ["basicpy"],
                     "description": "input that defines type of illumination correction to be performed"
+                },
+                "segmentation": {
+                    "type": "string",
+                    "pattern": "^((cellpose|mesmer)?,?)*(?<!,)$",
+                    "description": "comma separated list of segmentation modules to run. options are ['mesmer','cellpose']"
+                },
+                "cellpose_model": {
+                    "type": "string",
+                    "description": "optional model file for cellpose segmentation"
                 }
             }
         },
diff --git a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
index 9436592..6e14870 100644
--- a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
@@ -175,6 +175,11 @@ def validateInputParameters() {
     } else if(!params.input_sample && !params.input_cycle) {
         error "You must specify either input_sample or input_cycle."
     }
+
+    if (params.cellpose_model && !segmentation_list.contains('cellpose')) {
+        error "You can only provide a cellpose model if you have selected cellpose as one of your segmentation methods"
+    }
+
 }
 
 //
diff --git a/tests/main.nf.test b/tests/main.nf.test
index d212820..2baff99 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -9,6 +9,9 @@ nextflow_workflow {
         test("cycle: no illumination correction") {
 
             when {
+                params {
+                    segmentation = "mesmer"
+                }
                 workflow {
                     """
                     input[0] = Channel.of(
@@ -37,7 +40,7 @@ nextflow_workflow {
                         assert snapshot (
                             path("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
                         ).match()
                     },
                     { assert workflow.success }
@@ -51,6 +54,7 @@ nextflow_workflow {
             when {
                 params {
                     illumination = "basicpy"
+                    segmentation = "mesmer"
                 }
                 workflow {
                     """
@@ -80,7 +84,7 @@ nextflow_workflow {
                         assert snapshot (
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
-                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff")
                         ).match()
@@ -95,6 +99,7 @@ nextflow_workflow {
             when {
                 params {
                     illumination = "manual"
+                    segmentation = "mesmer"
                 }
                 workflow {
                     """
@@ -124,7 +129,7 @@ nextflow_workflow {
                         assert snapshot (
                             path("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv")
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv")
                         ).match()
                     },
                     { assert workflow.success }
@@ -135,6 +140,9 @@ nextflow_workflow {
         test("cycle: multiple file ashlar input no correction") {
 
             when {
+                params {
+                    segmentation = "mesmer"
+                }
                 workflow {
                     """
                     input[0] = Channel.of(
@@ -183,7 +191,7 @@ nextflow_workflow {
                         assert snapshot (
                             path("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv")
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv")
                         ).match()
                     },
                     { assert workflow.success }
@@ -194,6 +202,76 @@ nextflow_workflow {
         test("cycle: multiple file ashlar input with multiple samples no correction") {
 
             when {
+                params {
+                    segmentation = "mesmer"
+                }
+                workflow {
+                    """
+                    input[0] = Channel.of(
+                        [
+                            [id:"cycif-tonsil", cycle_number:1, channel_count:4],
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif",
+                            [],
+                            [],
+                        ],
+                        [
+                            [id:"cycif-tonsil", cycle_number:2, channel_count:4],
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif",
+                            [],
+                            [],
+                        ],
+                        [
+                            [id:"cycif-tonsil2", cycle_number:1, channel_count:4],
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif",
+                            [],
+                            [],
+                        ],
+                        [
+                            [id:"cycif-tonsil2", cycle_number:2, channel_count:4],
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif",
+                            [],
+                            [],
+                        ],
+                    )
+                    input[1] = Channel.of(
+                        [
+                            [1,1,'DNA_6',[],[],[]],
+                            [2,1,'ELANE',[],[],[]],
+                            [3,1,'CD57',[],[],[]],
+                            [4,1,'CD45',[],[],[]],
+                            [5,1,'DNA_7',[],[],[]],
+                            [6,1,'ELANE7',[],[],[]],
+                            [7,1,'CD577',[],[],[]],
+                            [8,1,'CD457',[],[],[]],
+                        ],
+                    )
+                    """
+                }
+            }
+
+            then {
+                assertAll (
+                    {
+                        assert snapshot (
+                            path("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
+                            path("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
+                            path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
+                            path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
+                        ).match()
+                    },
+                    { assert workflow.success }
+                )
+            }
+        },
+
+        test("cycle: multiple file ashlar input with multiple samples no correction, multiple segmentation") {
+
+            when {
+                params {
+                    segmentation = "mesmer,cellpose"
+                }
                 workflow {
                     """
                     input[0] = Channel.of(
@@ -246,8 +324,12 @@ nextflow_workflow {
                             path("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cycif-tonsil2_mask_cycif-tonsil2.csv"),
+                            path("$outputDir/segmentation/cellpose/cycif-tonsil.ome_cp_masks.tif"),
+                            path("$outputDir/segmentation/cellpose/cycif-tonsil2.ome_cp_masks.tif"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil_cycif-tonsil.csv"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil2_cycif-tonsil2.csv"),
                         ).match()
                     },
                     { assert workflow.success }
@@ -260,6 +342,7 @@ nextflow_workflow {
             when {
                 params {
                     illumination = "basicpy"
+                    segmentation = "mesmer"
                 }
                 workflow {
                     """
@@ -309,7 +392,7 @@ nextflow_workflow {
                         assert snapshot (
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
-                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
@@ -328,6 +411,7 @@ nextflow_workflow {
             when {
                 params {
                     illumination = "basicpy"
+                    segmentation = "mesmer"
                 }
                 workflow {
                     """
@@ -381,8 +465,8 @@ nextflow_workflow {
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
-                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
-                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil2_mask_cycif-tonsil2.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
@@ -396,5 +480,48 @@ nextflow_workflow {
             }
         },
 
+        test("cycle: no illumination correction, cellpose segmentation") {
+
+            when {
+                params {
+                    segmentation = "cellpose"
+                }
+                workflow {
+                    """
+                    input[0] = Channel.of(
+                        [
+                            [id:"TEST1", cycle_number:1, channel_count:4],
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif",
+                            [],
+                            [],
+                        ],
+                    )
+                    input[1] = Channel.of(
+                        [
+                            [1,1,'DNA_6',[],[],[]],
+                            [2,1,'ELANE',[],[],[]],
+                            [3,1,'CD57',[],[],[]],
+                            [4,1,'CD45',[],[],[]],
+                        ],
+                    )
+                    """
+                }
+            }
+
+            then {
+                assertAll (
+                    {
+                        assert snapshot (
+                            path("$outputDir/registration/ashlar/TEST1.ome.tif"),
+                            path("$outputDir/segmentation/cellpose/TEST1.ome_cp_masks.tif"),
+                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/TEST1_TEST1.csv"),
+                        ).match()
+                    },
+                    { assert workflow.success }
+                )
+            }
+
+        },
+
     ]
 }
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
index af16e98..28fcf73 100644
--- a/tests/main.nf.test.snap
+++ b/tests/main.nf.test.snap
@@ -87,6 +87,37 @@
         },
         "timestamp": "2024-04-23T11:52:51.734421588"
     },
+    "cycle: multiple file ashlar input with multiple samples no correction, multiple segmentation": {
+        "content": [
+            "cycif-tonsil.ome.tif:md5,9d4fca1d7ec97be3f6343eb712af9dea",
+            "cycif-tonsil2.ome.tif:md5,ea772fef41d398ffd76cbb6354266678",
+            "mask_cycif-tonsil.tif:md5,c1075eb025f558fcadedc1f0d903ec15",
+            "mask_cycif-tonsil2.tif:md5,bacaeced4f2159b8b7f3b42d173f995c",
+            "cycif-tonsil.ome_cp_masks.tif:md5,88690c63ef3b695f44e5bad40b8175a3",
+            "cycif-tonsil2.ome_cp_masks.tif:md5,c4590940d460cfe34168661573cfd87d",
+            "cycif-tonsil_mask_cycif-tonsil.csv:rounded:md5,5b5036130a84dc31268007aaf3322917",
+            "cycif-tonsil2_mask_cycif-tonsil2.csv:rounded:md5,61eb9b30399fb29041f2d080181b6e47",
+            "cycif-tonsil_cycif-tonsil.csv:rounded:md5,96c0754e24b8474d4c191bdff4351701",
+            "cycif-tonsil2_cycif-tonsil2.csv:rounded:md5,a53cf1c3df3ff3edfa93e1d266185701"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-07-09T14:19:05.560663388"
+    },
+    "cycle: no illumination correction, cellpose segmentation": {
+        "content": [
+            "TEST1.ome.tif:md5,ae98ac74e3c818bb26c99ba4b9c2dd51",
+            "TEST1.ome_cp_masks.tif:md5,47bd29c261db5fe062ee35c1b5daccc1",
+            "TEST1_TEST1.csv:rounded:md5,42ecd15013bea6dbea4e0343c7b0bef7"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-07-18T17:30:38.010217727"
+    },
     "cycle: multiple file ashlar input with basicpy correction": {
         "content": [
             {
@@ -219,6 +250,18 @@
         },
         "timestamp": "2024-04-23T11:53:19.871380893"
     },
+    "cycle: no illumination correction": {
+        "content": [
+            "TEST1.ome.tif:md5,ae98ac74e3c818bb26c99ba4b9c2dd51",
+            "mask_TEST1.tif:md5,c1075eb025f558fcadedc1f0d903ec15",
+            "TEST1_mask_TEST1.csv:rounded:md5,a7c226a3d32a94dd05356c5998eae522"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-22T15:58:40.245133922"
+    },
     "cycle: multiple file ashlar input with multiple samples and basicpy correction": {
         "content": [
             {
@@ -398,18 +441,6 @@
         },
         "timestamp": "2024-04-22T16:00:55.775911164"
     },
-    "cycle: no illumination correction": {
-        "content": [
-            "TEST1.ome.tif:md5,ae98ac74e3c818bb26c99ba4b9c2dd51",
-            "mask_TEST1.tif:md5,c1075eb025f558fcadedc1f0d903ec15",
-            "TEST1_mask_TEST1.csv:rounded:md5,a7c226a3d32a94dd05356c5998eae522"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-22T15:58:40.245133922"
-    },
     "cycle: manual illumination correction": {
         "content": [
             "TEST1.ome.tif:md5,ae98ac74e3c818bb26c99ba4b9c2dd51",
diff --git a/tests/workflows/mcmicro.nf.test b/tests/workflows/mcmicro.nf.test
index 71e12cf..bb92fda 100644
--- a/tests/workflows/mcmicro.nf.test
+++ b/tests/workflows/mcmicro.nf.test
@@ -7,6 +7,9 @@ nextflow_workflow {
     test("test 1") {
 
         when {
+            params {
+                segmentation = "mesmer"
+            }
             workflow {
                 """
                 input[0] = Channel.of(
diff --git a/workflows/mcmicro.nf b/workflows/mcmicro.nf
index 77e7b7c..1d6744d 100644
--- a/workflows/mcmicro.nf
+++ b/workflows/mcmicro.nf
@@ -76,13 +76,40 @@ workflow MCMICRO {
     // // Run Background Correction
     // BACKSUB(ASHLAR.out.tif, ch_markers)
     //BACKSUB(ASHLAR.out.tif, [[id: "backsub"], params.marker_sheet])
-    //ch_versions = ch_versions.mix(BACKSUB.out.versions)
+    /*
+    if (params.backsub) {
+        BACKSUB(ASHLAR.out.tif, [[id:"$ASHLAR.out.tif[0]['id']"], params.marker_sheet])
+        ch_segmentation_input = BACKSUB.out.backsub_tif
+        ch_versions = ch_versions.mix(BACKSUB.out.versions)
+    } else {
+    */
+        ch_segmentation_input = ASHLAR.out.tif
+    /*
+    }
+    */
 
     // Run Segmentation
 
-    DEEPCELL_MESMER(ASHLAR.out.tif, [[:],[]])
+    ch_masks = Channel.empty()
+
+    ch_segmentation_input
+        .multiMap{ meta, image ->
+            img: [meta + [segmenter: 'mesmer'], image]
+            membrane_img: [[:], []]
+        }
+        | DEEPCELL_MESMER
+    ch_masks = ch_masks.mix(DEEPCELL_MESMER.out.mask)
     ch_versions = ch_versions.mix(DEEPCELL_MESMER.out.versions)
 
+    ch_segmentation_input
+        .multiMap{ meta, image ->
+            image: [meta + [segmenter: 'cellpose'], image]
+            model: params.cellpose_model
+        }
+        | CELLPOSE
+    ch_masks = ch_masks.mix(CELLPOSE.out.mask)
+    ch_versions = ch_versions.mix(CELLPOSE.out.versions)
+
     // Run Quantification
 
     // Generate markers.csv for mcquant with just the marker_name column.
@@ -92,16 +119,19 @@ workflow MCMICRO {
             it.collect{ _1, _2, marker_name, _4, _5, _6 -> '"' + marker_name + '"' }
         }
         .collectFile(name: 'markers.csv', sort: false, newLine: true)
+
     ASHLAR.out.tif
-        .join(DEEPCELL_MESMER.out.mask)
+        .cross(ch_masks) { it[0]['id'] }
+        .map{ t_ashlar, t_mask -> [t_mask[0], t_ashlar[1], t_mask[1]] }
         .combine(ch_mcquant_markers)
-        .dump(tag: 'MCQUANT in')
-        .multiMap { it ->
-            image: [it[0], it[1]]
-            mask: [it[0], it[2]]
-            markers: [it[0], it[3]]
+        .dump(tag: 'MCQUANT IN')
+        .multiMap{ meta, image, mask, marker ->
+            image: [meta, image]
+            mask: [meta, mask]
+            markers: [meta, marker]
         }
         | MCQUANT
+
     ch_versions = ch_versions.mix(MCQUANT.out.versions)
 
     /*