Add palom as local module

conf/modules.config

@@ -36,8 +36,20 @@ process {
         ]
     }
 
+    withName: ALIGNMULTIPLECYCLES {
+        ext.args = { params.palom_align_channel ? "--channel ${params.palom_align_channel}" : ''}
+        // TODO px_size specification?
+        ext.when = {params.registration_method.split(',').contains('palom')}
+        publishDir = [
+            path: { "${params.outdir}/registration/palom" },
+            mode: params.publish_dir_mode,
+        ]
+    }
+
+
     withName: ASHLAR {
         containerOptions = '--user root'
+        ext.when = {params.registration_method.split(',').contains('ashlar')}
         publishDir = [
             path: { "${params.outdir}/registration/ashlar" },
             mode: params.publish_dir_mode,

modules/local/palom/alignmultiplecycles/environment.yml

@@ -0,0 +1,11 @@
+name: "palom_multicycle"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "openslide=4.0.0"
+  - "scikit-image=0.19.3"
+  - pip
+  - pip:
+      - "palom==2024.4.1"

modules/local/palom/alignmultiplecycles/main.nf

@@ -0,0 +1,43 @@
+process ALIGNMULTIPLECYCLES {
+    tag "$meta.id"
+    label 'process_single'
+    container "docker.io/voigtgesa/palom:v2024.4.1_cli2"
+
+    input:
+    tuple val(meta), path(images, stageAs: 'image*/*')
+
+    output:
+    tuple val(meta), path("*.ome.tif"), emit: tif
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args          = task.ext.args           ?: ''
+    def prefix        = task.ext.prefix         ?: "${meta.id}"
+
+    """
+    python /palom/align_multiple_cycles.py \\
+        --img_list $images \\
+        --out_name ${prefix}.ome.tif \\
+        --out_dir . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        palom: \$(palom-svs --version | sed 's/palom v//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.ome.tif
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        palom: \$(palom-svs --version | sed 's/palom v//')
+    END_VERSIONS
+    """
+}

modules/local/palom/alignmultiplecycles/meta.yml

@@ -0,0 +1,47 @@
+name: "palom_multiplecycles"
+description: Alignment for Multiple Layers of Mosaics
+keywords:
+  - image_processing
+  - registration
+  - alignment
+tools:
+  - "palom":
+      description: "Piecewise Alignment for Layers of Mosaics. Palom started as a tool for registering whole-slide images of the same FFPE section with different IHC stainings"
+      homepage: "https://github.com/labsyspharm/palom"
+      documentation: "https://github.com/labsyspharm/palom/blob/main/README.md"
+      tool_dev_url: "https://github.com/labsyspharm/palom"
+      doi: ""
+      licence: "" ## TODO Wait for licence specification (opened issue)
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - images:
+      type: path
+      description: List of paths to OME-TIF files, ordered by consecutive imaging cycles
+      pattern: "*.{ome.tiff,ome.tif,tif,tiff}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1']`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tif:
+      type: file
+      description: Registered image
+      pattern: "*.ome.tif"
+
+authors:
+  - "@kbestak"
+  - "@gesavoigt"
+maintainers:
+  - "@kbestak"
+  - "@gesavoigt"

nextflow.config

@@ -15,6 +15,8 @@ params {
     marker_sheet               = null
     segmentation               = 'mesmer'
     cellpose_model             = []
+    registration_method        = 'ashlar'
+    palom_align_channel        = 0
 
     // Illumination correction
     illumination               = null

nextflow_schema.json

@@ -69,11 +69,24 @@
                 "segmentation": {
                     "type": "string",
                     "pattern": "^((cellpose|mesmer)?,?)*(?<!,)$",
-                    "description": "comma separated list of segmentation modules to run. options are ['mesmer','cellpose']"
+                    "description": "comma separated list of segmentation modules to run. options are ['mesmer','cellpose']",
+                    "default": "mesmer"
                 },
                 "cellpose_model": {
                     "type": "string",
-                    "description": "optional model file for cellpose segmentation"
+                    "description": "optional model file for cellpose segmentation",
+                    "default": "[]"
+                },
+                "registration_method": {
+                    "type": "string",
+                    "default": "ashlar",
+                    "pattern": "^((ashlar|palom)?,?)*(?<!,)$",
+                    "description": "Registration method to be used (ashlar or palom)"
+                },
+                "palom_align_channel": {
+                    "type": "integer",
+                    "default": 0,
+                    "description": "Channel to use for image registration"
                 }
             }
         },

workflows/mcmicro.nf

@@ -13,6 +13,7 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_mcmicro_pipeline'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { BASICPY                } from '../modules/nf-core/basicpy/main'
+include { ALIGNMULTIPLECYCLES    } from '../modules/local/palom/alignmultiplecycles/main'
 include { ASHLAR                 } from '../modules/nf-core/ashlar/main'
 include { BACKSUB                } from '../modules/nf-core/backsub/main'
 include { CELLPOSE               } from '../modules/nf-core/cellpose/main'
@@ -56,6 +57,24 @@ workflow MCMICRO {
             .dump(tag: 'ch_samplesheet (after BASICPY)')
     }
 
+    // Image registration
+    ch_registration = Channel.empty()
+
+    ch_samplesheet
+        .map{ meta, image_tiles, dfp, ffp ->
+            [[id: meta.id], [meta.cycle_number, image_tiles]]
+        }
+        // FIXME: pass groupTuple size: from samplesheet cycle count
+        .groupTuple(sort: { a, b -> a[0] <=> b[0] })
+        .map{ meta, cycles -> [meta, *cycles.collect{ it[1..-1] }.transpose()]}
+        .dump(tag: 'PALOM in')
+        | ALIGNMULTIPLECYCLES
+    if (params.registration_method.split(',').contains('palom')) {
+        ch_versions = ch_versions.mix(ALIGNMULTIPLECYCLES.out.versions)
+        ch_registration = ch_registration.mix(ALIGNMULTIPLECYCLES.out.tif)
+    }
+
+
     ch_samplesheet
         .map{ meta, image_tiles, dfp, ffp ->
             [[id: meta.id], [meta.cycle_number, image_tiles, dfp, ffp]]
@@ -72,6 +91,10 @@ workflow MCMICRO {
         }
         | ASHLAR
     ch_versions = ch_versions.mix(ASHLAR.out.versions)
+    if (params.registration_method.split(',').contains('ashlar')) {
+        ch_versions = ch_versions.mix(ASHLAR.out.versions)
+        ch_registration = ch_registration.mix(ASHLAR.out.tif)
+    }
 
     // // Run Background Correction
     // BACKSUB(ASHLAR.out.tif, ch_markers)
@@ -83,7 +106,8 @@ workflow MCMICRO {
         ch_versions = ch_versions.mix(BACKSUB.out.versions)
     } else {
     */
-        ch_segmentation_input = ASHLAR.out.tif
+        ch_registration.view()
+        ch_segmentation_input = ch_registration
     /*
     }
     */