changes for cell or nucleus segmentation

Author: khersameesh24

modules/nf-core/cellpose/cellpose.diff

@@ -22,7 +22,8 @@ params {
 
     // execution specific
     sharpen_tiff               = false      // wether to sharpen the morphology-focus tiff
-    nucleus_segmentation_only  = false      // to only run nucleus segmentation while running XR_IMP-SEG
+    nucleus_segmentation_only  = false      // to only run nucleus segmentation while running segmentation methods & XR_IMP-SEG
+    cell_segmentation_only     = true       // to only run cell segmentation while running segmentation methods & XR_IMP-SEG
 
     // Xeniumranger specific
     xeniumranger_only          = false      // to generate redefined bundle with just changing the xr specific params

nextflow.config

@@ -20,7 +20,7 @@ workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
     ch_versions = Channel.empty()
 
     // run cellpose to generate segmentation mask
-    CELLPOSE ( ch_morphology_image, [])
+    CELLPOSE ( ch_morphology_image, [], [])
     ch_versions = ch_versions.mix ( CELLPOSE.out.versions )
 
 

subworkflows/local/cellpose_baysor_import_segmentation/main.nf

@@ -28,7 +28,7 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
 
         // run cellpose on the enhanced tiff
         CELLPOSE_CELLS ( RESOLIFT.out.enhanced_tiff, cellpose_model, 'cells' )
-        ch_versions = ch_versions.mix( CELLPOSE.out.versions )
+        ch_versions = ch_versions.mix( CELLPOSE_CELLS.out.versions )
 
         CELLPOSE_NUCLEI ( RESOLIFT.out.enhanced_tiff, 'nuclei', 'nuclei' )
         ch_versions = ch_versions.mix( CELLPOSE_NUCLEI.out.versions )

subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf

@@ -153,6 +153,14 @@ workflow SPATIALXE {
         )
     }
 
+    // get custom cellpose model if provided with the --cellpose_model for the cellpose method
+    if ( params.cellpose_model ) {
+        ch_features = Channel.fromPath (
+            params.cellpose_model,
+            checkIfExists: true
+        )
+    }
+
     // get gene_panel.json if provided with --gene_panel, sets relabel_genes to true
     if (( params.gene_panel )) {