A QuPath script to make cell objects from lists of cytos and nuclei

make_cells_from_cytos_and_nuclei.groovy

cytos = getDetectionObjects().findAll{it.getPathClass() == getPathClass('cells')}
nuclei = getDetectionObjects().findAll{it.getPathClass() == getPathClass('nuclei')}

print cytos
print nuclei

// Combine cytos and nuclei detections to create cell objects
def cells = cytos.collect{ cyto -> 
      cell_nucs = nuclei.findAll{ nuc -> cyto.getROI().contains( nuc.getROI().getCentroidX() , nuc.getROI().getCentroidY() )} 
      if ( !cell_nucs.isEmpty() ) {
          // it happens that a cell contains more than one nuclei // Don't ask why ;) 
          // we merge the nuclei in one object
          nuc = PathObjectTools.mergeObjects(cell_nucs)
          // create the cell
          cell = PathObjects.createCellObject(cyto.getROI(), nuc.getROI(), getPathClass("Cellpose"), null ) 
          //and add the the nuclei count as measurement
          cell.measurements["Nuclei : Count "] =  cell_nucs.size()
          return cell
      } else {
          //return null
      }
}.findAll{it!=null}

clearDetections() 
addObjects( cells )