Couple of fixes

conf/modules.config

@@ -138,7 +138,25 @@ process {
             path: { "${params.outdir}/cellpose" },
             mode: params.publish_dir_mode,
         ]
-        ext.args = { "--pretrained_model nuclei --diameter 9 --channel_axis 0 --save_flows" }
+        ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
+    }
+
+    // with new version of cellpose you can do --output_name cell_masks
+    withName: CELLPOSE_CELLS {
+        publishDir = [
+            path: { "${params.outdir}/cellpose_cells" },
+            mode: params.publish_dir_mode,
+        ]
+        ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
+    }
+
+    // with new version of cellpose you can do --output_name nucleus_masks
+    withName: CELLPOSE_NUCLEI {
+        publishDir = [
+            path: { "${params.outdir}/cellpose_nuclei" },
+            mode: params.publish_dir_mode,
+        ]
+        ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
     }
 
 }

modules/local/spatialdata/write/main.nf

@@ -7,6 +7,7 @@ process SPATIALDATA_WRITE {
     input:
     tuple val(meta), path(bundle, stageAs: "*")
     val(outputfolder)
+    val(segmented_object)
 
     output:
     tuple val(meta), path("${outputfolder}"), emit: spatialdata

modules/local/spatialdata/write/templates/write.py

@@ -12,14 +12,34 @@ def main():
     input_path = "${bundle}"
     output_path = "."
     outputfolder = "${outputfolder}"
+    segmented_object = "${segmented_object}"
+
+    cells_boundaries=False
+    nucleus_boundaries=False
+    cells_labels=False
+    nucleus_labels=False
+
+    if ( segmented_object == 'cells' ):
+        cells_boundaries=True
+        cells_labels=True
+    if ( segmented_object == 'nuclei' ):
+        nucleus_boundaries=True
+        nucleus_labels=True
+    if ( segmented_object == 'cells_and_nuclei' ):
+        cells_boundaries=True
+        nucleus_boundaries=True
+        cells_labels=True
+        nucleus_labels=True
 
     format = "${params.format}"
-
     if ( format == "xenium" ):
         sd_xenium_obj = xenium(
             input_path,
             cells_as_circles=True,
-            nucleus_boundaries=True,
+            cells_boundaries=cells_boundaries,
+            nucleus_boundaries=nucleus_boundaries,
+            cells_labels=cells_labels,
+            nucleus_labels=nucleus_labels,
             transcripts=True,
             morphology_mip=True,
             morphology_focus=True,

subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf

@@ -2,7 +2,8 @@
 // Run cellpose on the morphology tiff
 //
 
-include { CELLPOSE                         } from '../../../modules/nf-core/cellpose/main'
+include { CELLPOSE as CELLPOSE_CELLS       } from '../../../modules/nf-core/cellpose/main'
+include { CELLPOSE as CELLPOSE_NUCLEI      } from '../../../modules/nf-core/cellpose/main'
 include { RESOLIFT                         } from '../../../modules/local/resolift/main'
 include { XENIUMRANGER_IMPORT_SEGMENTATION } from '../../../modules/nf-core/xeniumranger/import-segmentation/main'
 
@@ -26,24 +27,39 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
         ch_versions = ch_versions.mix( RESOLIFT.out.versions )
 
         // run cellpose on the enhanced tiff
-        CELLPOSE ( RESOLIFT.out.enhanced_tiff, cellpose_model )
+        CELLPOSE_CELLS ( RESOLIFT.out.enhanced_tiff, cellpose_model, 'cells' )
         ch_versions = ch_versions.mix( CELLPOSE.out.versions )
 
+        CELLPOSE_NUCLEI ( RESOLIFT.out.enhanced_tiff, 'nuclei', 'nuclei' )
+        ch_versions = ch_versions.mix( CELLPOSE_NUCLEI.out.versions )
+
     } else {
 
         // run cellpose on the original tiff
-        CELLPOSE ( ch_morphology_image, cellpose_model )
-        ch_versions = ch_versions.mix( CELLPOSE.out.versions )
+        CELLPOSE_CELLS ( ch_morphology_image, cellpose_model, 'cells' )
+        ch_versions = ch_versions.mix( CELLPOSE_CELLS.out.versions )
+
+        CELLPOSE_NUCLEI ( ch_morphology_image, 'nuclei', 'nuclei' )
+        ch_versions = ch_versions.mix( CELLPOSE_NUCLEI.out.versions )
     }
 
     // get cellpose segmentation results
-    cellpose_cells = CELLPOSE.out.cells.map {
+    cellpose_cells_cells = CELLPOSE_CELLS.out.cells.map {
+        _meta, cells -> return [ cells ]
+    }
+    cellpose_cells_mask = CELLPOSE_CELLS.out.mask.map {
+        _meta, mask -> return [ mask ]
+    }
+    _cellpose_cells_flows = CELLPOSE_CELLS.out.flows.map {
+        _meta, flows -> return [ flows ]
+    }
+    cellpose_nuclei_cells = CELLPOSE_NUCLEI.out.cells.map {
         _meta, cells -> return [ cells ]
     }
-    cellpose_mask = CELLPOSE.out.mask.map {
+    cellpose_nuclei_mask = CELLPOSE_NUCLEI.out.mask.map {
         _meta, mask -> return [ mask ]
     }
-    _cellpose_flows = CELLPOSE.out.flows.map {
+    _cellpose_nuclei_flows = CELLPOSE_NUCLEI.out.flows.map {
         _meta, flows -> return [ flows ]
     }
 
@@ -53,7 +69,7 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
         XENIUMRANGER_IMPORT_SEGMENTATION (
             ch_bundle_path,
             [],
-            cellpose_mask,
+            cellpose_nuclei_mask,
             [],
             [],
             [],
@@ -66,8 +82,8 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
         XENIUMRANGER_IMPORT_SEGMENTATION (
             ch_bundle_path,
             [],
-            cellpose_mask,
-            cellpose_cells,
+            cellpose_nuclei_mask,
+            cellpose_cells_mask,
             [],
             [],
             ""
@@ -77,9 +93,12 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
 
     emit:
 
-    mask  = CELLPOSE.out.mask                                      // channel: [ val(meta), [ "*masks.tif" ] ]
-    flows = CELLPOSE.out.flows                                     // channel: [ val(meta), [ "*flows.tif" ] ]
-    cells = CELLPOSE.out.cells                                     // channel: [ val(meta), [ "*seg.npy" ] ]
+    cells_mask  = CELLPOSE_CELLS.out.mask                                // channel: [ val(meta), [ "*masks.tif" ] ]
+    cells_flows = CELLPOSE_CELLS.out.flows                               // channel: [ val(meta), [ "*flows.tif" ] ]
+    cells_cells = CELLPOSE_CELLS.out.cells                               // channel: [ val(meta), [ "*seg.npy" ] ]
+    nuclei_mask  = CELLPOSE_NUCLEI.out.mask                              // channel: [ val(meta), [ "*masks.tif" ] ]
+    nuclei_flows = CELLPOSE_NUCLEI.out.flows                             // channel: [ val(meta), [ "*flows.tif" ] ]
+    nuclei_cells = CELLPOSE_NUCLEI.out.cells                             // channel: [ val(meta), [ "*seg.npy" ] ]
 
     redefined_bundle = XENIUMRANGER_IMPORT_SEGMENTATION.out.bundle // channel: [ val(meta), ["redefined-xenium-bundle"] ]
 

subworkflows/local/spatialdata_write_meta_merge/main.nf

@@ -10,8 +10,9 @@ include { SPATIALDATA_META                                        } from '../../
 workflow SPATIALDATA_WRITE_META_MERGE {
 
     take:
-    ch_bundle_path      // channel: [ val(meta), [ "path-to-xenium-bundle" ] ]
-    ch_redefined_bundle // channel: [ val(meta), [ "redefined-xenium-bundle" ] ]
+    ch_bundle_path          // channel: [ val(meta), [ "path-to-xenium-bundle" ] ]
+    ch_redefined_bundle     // channel: [ val(meta), [ "redefined-xenium-bundle" ] ]
+    ch_segmented_object     // can be either cells,nuclei,cells_and_nuclei
 
     main:
 
@@ -20,15 +21,17 @@ workflow SPATIALDATA_WRITE_META_MERGE {
     // write spatialdata object from the raw xenium bundle
     SPATIALDATA_WRITE_RAW_BUNDLE (
         ch_bundle_path,
-        'spatialdata_raw'
+        'spatialdata_raw',
+        ch_segmented_object
     )
     ch_versions = ch_versions.mix ( SPATIALDATA_WRITE_RAW_BUNDLE.out.versions )
 
 
     // write spatialdata object after running IMP_SEG
     SPATIALDATA_WRITE_REDEFINED_BUNDLE (
         ch_redefined_bundle,
-        'spatialdata_redefined'
+        'spatialdata_redefined',
+        ch_segmented_object
     )
     ch_versions = ch_versions.mix ( SPATIALDATA_WRITE_REDEFINED_BUNDLE.out.versions )
 

subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf

@@ -195,13 +195,6 @@ def validateInputParameters() {
         log.warn "⚠️  Use --nucleus_segmentation_only to enable nucleus segmentation to redefine xenium bundle with import-segmentation module."
     }
 
-    if ( params.mode == 'image' && params.method == 'baysor' ) {
-        if ( !params.method_mask ) {
-            log.error "❌ Error: Missing path to segmentation mask. Image-based segmentation with the `baysor` method requires a segmentation mask with the `--segmentation_mask` option."
-            exit 1
-        }
-    }
-
 }
 
 //

workflows/spatialxe.nf

@@ -241,12 +241,21 @@ workflow SPATIALXE {
             // run baysor run with morphology_ome.tif
             if ( params.method == 'baysor' ) {
 
-                BAYSOR_RUN_PRIOR_SEGMENTATION_MASK (
-                    ch_bundle_path,
-                    ch_transcripts_parquet,
-                    ch_segmentation_mask,
-                    ch_config
-                )
+                if ( params.segmentation_mask ) {
+                    BAYSOR_RUN_PRIOR_SEGMENTATION_MASK (
+                        ch_bundle_path,
+                        ch_transcripts_parquet,
+                        ch_segmentation_mask,
+                        ch_config
+                    )
+                } else {
+                    BAYSOR_RUN_PRIOR_SEGMENTATION_MASK (
+                        ch_bundle_path,
+                        ch_transcripts_parquet,
+                        [],
+                        ch_config
+                    )
+                }
                 ch_redefined_bundle = BAYSOR_RUN_PRIOR_SEGMENTATION_MASK.out.redefined_bundle
             }
 
@@ -343,9 +352,12 @@ workflow SPATIALXE {
     // run spatialdata modules to generate sd objects in image or coordinate mode
     if ( params.mode == 'image' || params.mode == 'coordinate' ) {
 
+        ch_segmented_object = Channel.value('cells_and_nuclei')
+
         SPATIALDATA_WRITE_META_MERGE (
             ch_bundle_path,
-            ch_redefined_bundle
+            ch_redefined_bundle,
+            ch_segmented_object
         )
 
     }