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Joe Chalfoun

Senior Research Scientist

Joe Chalfoun works as a research contractor for the National Institute of Standards and Technology Federal Department of Commerce where he is part of a Computational Science in Biological Metrology project that studies cell microscopy and image analysis of cellular protein dynamics and expression in individual cells. His work includes studying the uncertainty and accuracy of most popular segmentation techniques utilized by the biologist to segment cell images, creating an overlap based cell tracker to track live cells and study dynamic behavior of protein expressions, and creating a general technique for accurately stitching large dataset, the purpose of which is to locate stem cell colonies on a plate and study the entire population Oct4 expression.

His work also includes identifying sub-cellular features on high magnification cell images with different background stiffness using region growing and clustering techniques. This study was made to establish a first correlation of the sub-cellular features between multiple protein expressions and their usage to determine the classification of cells. He also worked to establish a feedback loop from image analysis to the microscope controller software that enabled the automation of acquiring high throughput images of high quality and high magnification cell images with all cells of interest centered in the middle of the field of view. This helped increase the accuracy of subcellular feature analysis and saved hundreds of man-hour spent to acquire similar images.

Joe has also worked as a Guest Research Scientist for NIST where he worked on a project that simultaneously compared mass artifacts in air and vacuum using a high precision mass comparator. The system uses a magnetic levitation technique as a link between the vacuum and air. The magnetic levitation system used was formed by two permanent magnets and a solenoid to maintain stable levitation. Joe worked to optimize the magnetic levitation control to achieve higher levitation accuracy which lead to a higher stability in the balance reading and to a levitation stability up to 3 micrometers in vertical oscillations. He also designed some of the system parts needed for the rotation control of the levitated body as well as a special hoist lifting structure needed to assemble or dismantle the system. Further work includes assembling the entire structure that included a bell Jar, the upper and lower chambers and the vacuum pumping lines, testing the vacuum level in the chambers, pumping the lines for leaks, and making a mechanical animation of the entire process using SolidWorks. The animation also included a future work that involves a transporter used to transport a mass artifact in vacuum from outside the chamber and places it inside the vacuum chamber on the mass pan of the balance. The transporter used a robotic arm to manipulate the artifact.

Another part of this project involved the optimization of the gap and overlap between two permanent magnet’s shielding. This part was achieved in simulation by interoperability between MagNet, Matlab and Excel by using visual basic. MagNet was used for magnetic calculation, Matlab for optimization, and Excel as an interface for the inputs and outputs.

Before his work with Prometheus Computing and NIST, Joe worked as a Research Scientist at the CEA (Atomic Energy Commission) in France where he worked on a research project taking place in the Remote Handling activities for the next fusion reactor ITER. The aim of this project was to develop a flexible model of the long reach articulated carrier, known as the AIA robot, in order to compensate its flexibilities. This model has the particularity to be a physical model which inputs are the geometric and the stiffness parameters and the output is the geometric configurations of the arm including the end effector’s position. The aim was to increase the position accuracy of the end effector and the intermediate segments as well. The robot will be used for nuclear applications, mainly the inspection of the material inside the nuclear reactor. Joe’s work on the project included developing a flexible modeling of the long reach articulated carrier (in MATLAB) that takes into account most of the structure deformations, making the calibration of the robot using a nonlinear optimization procedure (in mex: C++ and MATLAB) in order to determine the parameters of the robot by experimental identification, and taking experimental measurements of the end effector’s position and orientation using a LEICA laser tracker. Joe also worked to create a patent that uses a double calibration method of the robot, which is a calibration of the flexible parameters followed by a second calibration method of the robot using generalized error matrices that is applied to further reduce the residual positioning error of the system.

Before his time at CEA, Joe worked as a Doctoral research assistant at L.I.R.I.S. Laboratory, at the University of Versailles Saint-Quentin and the National Center for Scientific Research in France. The research project for his Ph.D. involved the real-time simulation of the human hand and the forearm. The dynamic prediction of the muscle forces responsible for a given movement of the system was the aim of his doctoral thesis. The objective of the simulator SHARMES was based on the highly realistic reproduction of the movement of the human hand and the forearm system. His work included working with surgeons to define the biomechanical model of the human hand and forearm, creating a relation between muscle forces and the joints torques, predicting the muscle forces, activations and displacements during a given movement, and investigating multiple optimization techniques. Joe also worked in realizing the simulation of the system in real-time using C++ and quantitative validation between the predicted muscles activation and those coming from EMG (electromyography) signals. Joe worked as a research assistant at the Mechatronics Laboratory of Lebanese University with the Faculty of Engineering. Here he conducted a study of chatter vibrations during metal cutting and proposed new solutions to the vibration problem on the rotary cutting machines. Joe also worked with Mechatronics Laboratory at Lebanese University in conjunction with the Technological University of Compiègne, France. This work included conducting a survey of metal cutting constraints with finite elements. This work was selected as the best work of the year by both universities.

Joe has also worked as an automatic control systems engineer with YL Engineering Industry where he designed and built a prototype of a marble cutting machine, identified the system formed by the two motors, developed an automatic control system, and tested it.

Joe received his Ph.D. in Mechanical-Robotics Engineering from the University of Versailles Saint-Quentin, France in April 2005. For his work, Joe received the Distinguished University of Versailles thesis Honors, “Très Honorable avec les félicitations du jury,” an honor only ten percent of the graduated Ph.D. students in France are awarded.

Thesis: Muscle forces prediction in the hand and forearm system: modeling, simulation, optimization and validation.

Joe gained his M.S. in Mechanical Engineering (Industrial Control) from the University of Technology of Compiègne (UTC), France and the Lebanese University, Lebanon in September 2001. His project was a survey of metal cutting constraints with finite elements and his work won best project of the year.

Joe earned his B.S. in Mechanical Engineering from Lebanese University, Engineering School, Department of Mechanical Engineering in September 2000. His project was the identification and control of a marble saw for which he received high honors. Joe has supervising experience gained from his work with graduate school student in image analysis research, summer students on the live cell work and the microscope control for three summers in 2010 and 2011 and 2012, a Master’s degree student at the University of Versailles Saint-Quentin through a project on muscle forces prediction in the hand for the pinch movement, and an engineering student at Lebanese University during a project on heat transfer in the material during metal cutting.

Joe has also worked as a Teaching Assistant at the University of Versailles Saint-Quentin, where he worked in the department of computer science. At the University of Versailles Saint-Quentin Joe taught an undergraduate level mathematics courses, developed tests, graded assignments and exams, and earned a Certificate Distinction in Teaching. Joe also worked as a Teaching Assistant in the university’s Department of Mechanics where he taught various undergraduate level mechanics courses. These courses included fluid mechanics, solid dynamics, and mechanical design. His responsibilities included teaching, developing tests and grading exams.

Joe’s skills include mechanics and robotics, biomechanics modeling, design, dynamic study, simulation, optimization, finite elements, numerical analysis, automation, identification and mathematical modeling, adaptive control, image processing, segmentation, tracking, clustering, classification, and microscope experimental design.

He has full experience with MATLAB, Simulink, Mex, and SolidWorks, and good experience: with Maple, Mathematica, LabVIEW, Visual Basic, and Solid Dynamics. He speaks English, French, and Lebanese.

Patent: Projet BD 1773 (MCF 9813) “Procédé de calibration de la position la position d’un système poly-articulé, notamment d’un robot.” This patent concerns the improvement of the position accuracy of any poly-articulated robot.

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