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Hi all, Thank you Martins for recommendations. I answer my own question for those who are interested by the topic:

You can create in few lines a 3D viewer on which you can add point clouds and shapes : Please refer to the official tutorials for details http://pointclouds.org/documentation/tutorials/pcl_visualizer.php

/* generic 3D viewer display, similar to the official tutorials. changes added : camera setup :

_ use the viewer->resetCameraViewpoint("Considered blobs"); to point to the middle of your point cloud

_ use viewer->setCameraPosition (cameraPoxitionX, cameraPoxitionY, cameraPoxitionZ, viewX, viewY, viewZ) // to set the camera position and its directions

*/

Consider the following includes... first check your system configuration (add pcl library and dependencies),

#include <pcl/common/common_headers.h>
#include <pcl/point_cloud.h>
#include <pcl/impl/point_types.hpp>>
#include <pcl/io/pcd_io.h>
#include <pcl/visualization/pcl_visualizer.h>
#include <boost/thread/thread.hpp>

// This method display 3D COLOURED points

boost::shared_ptr<pcl::visualization::PCLVisualizer> createVisualizer (pcl::PointCloud<pcl::PointXYZRGB>::ConstPtr cloud)
{

    boost::shared_ptr<pcl::visualization::PCLVisualizer> viewer (new pcl::visualization::PCLVisualizer ("3D Viewer"));
    viewer->setBackgroundColor (0, 0, 0);
    pcl::visualization::PointCloudColorHandlerRGBField<pcl::PointXYZRGB> rgb(cloud);
    viewer->addPointCloud<pcl::PointXYZRGB> (cloud, rgb, "myPoints");
    viewer->setPointCloudRenderingProperties (pcl::visualization::PCL_VISUALIZER_POINT_SIZE, 3, "myPoints");
    viewer->addCoordinateSystem ( 1.0 );
    viewer->initCameraParameters ();
    viewer->resetCameraViewpoint("myPoints"); // camera points to the center of the point cloud
    viewer->setCameraPosition   (   camXPos, camXPos, camXPos, // camera position

            0, 1, 0 // camera direction to cloud center
            );  // ... then camera faces the point cloud
    return (viewer);
}

Once prepared and considering a cv::Mat image "colorImage" and a binary mask "areas" , add points to your point cloud and display it : ... take care of X&Y inversions (take into account the top left (0,0) of cv::Mat reference points) ...HINT, the Z axis can be used as the temporal information like in this exemple (time is refered as "frameIndex" here

Allocate your point cloud :

pcl::PointCloud<pcl::PointXYZRGB>::ConstPtr point_cloud_ptr(new pcl::PointCloud<pcl::PointXYZRGB>);

Fill the point cloud with the localizes and coloured segmented blob points

        for(int y=0;y<colorImage.rows;++y)
            for(int x=0;x<colorImage.cols;++x)
            {
                // get pixel data
                cv::Scalar maskPoint = areas.at<unsigned char>(cv::Point2d(x,y));
                cv::Vec3b colorPoint = colorImage.at<cv::Vec3b>(cv::Point2d(x,y));

                if (maskPoint[0])
                {
                    //std::cout<<"New point (x,y,z) = "<<x<<", "<<y<<", "<<frameIndex
                    //      <<" // (r,g,b) = "<<(int)pr<<", "<<(int)pg<<", "<<(int)pb<<std::endl;

                    //Insert info into point cloud structure
                    pcl::PointXYZRGB point;
                    point.x = -x;
                    point.y = -y;
                    point.z = frameIndex;
                    uint32_t rgb = (static_cast<uint32_t>(colorPoint.val[2]) << 16 |
                            static_cast<uint32_t>(colorPoint.val[1]) << 8 | static_cast<uint32_t>(colorPoint.val[0]));
                    point.rgb = *reinterpret_cast<float*>(&rgb);
                    point_cloud_ptr->points.push_back (point);
                }
            }

Finally, when the cloud is ready, display it by calling the first procedure :

... check doc to add any supplementary shape, here, a cude is added (dims are image size*timeLength).

    std::cout<<"Pointcould size : "<<point_cloud_ptr->points.size()<<std::endl;
    boost::shared_ptr<pcl::visualization::PCLVisualizer> viewer = createVisualizer( point_cloud_ptr );
    viewer->addCube (-colorImage.cols, 0, -colorImage.rows, 0, 0, timeLength);
    //Main user interaction waiting loop
    while ( !viewer->wasStopped())
    {
        viewer->spinOnce(100);
        boost::this_thread::sleep (boost::posix_time::microseconds (100000));
    }
    viewer->close(); // kill viewer
    viewer.reset();