Phd Activity of Vicidomini Giuseppe

Leave of Absence

Phd Courses and Credits

1. 7-18/03/2005. Scuola Internazionale dei Dottorandi di Informatica, Bertinoro (BO), Italy
   • Approximation, Chance and Networks (ACN) (15 h)
     Prof. Alessandro Panconesi, Dipartimento di Informatica University of Rome "La Sapienza", Italy.
     Exam: 29/30 
   • Machine Learning (ML) (15 h)
     Prof. Alessandro Sperduti, Dipartimento di Matematica Pura ed Applicata, University of Padova, Italy.
     Exam: - 
   • Decision diagrams and their applications (DDTA) (15 h)
     Prof. Gianfranco Ciardo, Department of Computer Science and Engineering, University of California at Riverside, USA.
     Exam: 98/100
   • Strong static typing and advanced functional programming (SST) (15 h) 
     Dr. Francesco Zappa Nardelli, INRIA Rocquencourt, France.
     Exam: - 
2. 2005. Inverse Problem: Theory and Application (21 h).
   Prof. Michele Piana. Depatment of Mathematics (DIMA). University of Genoa. Italy.
   Exam: -
3. 2006. Numerical Methods for Solving Differential Equation (21 h). 
   Prof.ssa  Patrizia Bagnerini. Dipartimento di Ingegneria della Produzione Termoenergetica e Modelli Matematici (DIPTEM). University of Genoa. Italy.
   Exam: accomplished
4. 2006. Machine Learning (15 h). 
   Ing. Marco Muselli. Consiglio Nazionale delle Ricerche. Istituto di Elettronica e di Ingegneria dell'Informazione e delle Telecomunicazioni (IEIIT). Sezione di Genova. Italy. 
   Exam: 18/20
5. 2006. Statistic and Nonlinear Regression (18 h). 
   Ing. Cristiano Cervellera. Consiglio Nazionale delle Ricerche. Istituto di Studi per Sistemi Intelligenti per Automazione (ISSIA). Sezione di Genova. Italy. 
   Exam: 16/20

Teaching Assistant Activity

• 25-29/6/2007
  Principles of Fluorescence Techniques Course. Edition V. University of Genoa. Laboratory Supervisor in Fluorescence Microscopy.
• 19-22/6/2006
  Principles of Fluorescence Techniques Course. Edition IV. University of Genoa. Laboratory Supervisor in Fluorescence Microscopy.
• 13-16/9/2005
  Principles of Fluorescence Techniques Course. Edition III. University of Genoa. Laboratory Supervisor in Fluorescence Microscopy.
• 9/2004-9/2005
  First level Master in  ”MICROSCOPIE ED ANALISI MICROSCOPICHE IN BIOLOGIA”. First Edition. University of Genoa. Faculty of Mathematical, Physical and Natural Science. Laboratory Supervisor in Fluorescence Microscopy.
• 9/2005-9/2006
  First level Master in ”MICROSCOPIE ED ANALISI MICROSCOPICHE IN BIOLOGIA”. Second Edition. University of Genoa. Faculty of Mathematical, Physical and Natural Science. Laboratory Supervisor in Fluorescence Microscopy.

Research Activity

• Supervisor: Patrizia Boccacci
• Thesis Advisor: Patrizia Boccacci
• Research interests: Inverse Problems in 3D microscopy

Pubblications

Journals

• G. Vicidomini, P. Boccacci, A. Diaspro, M. Bertero. Edge-preserving image restoration in confocal and two-photon excitation microscopy. In preparation.
• G. Vicidomini, M. C. Gagliani, M. Canfora, K. Cortese, F. Frosi, C. Santangelo, P. P. Di Fiore, P. Boccacci, A. Diaspro and C. Tacchetti. A novel High Data Output and 3D Correlative Microscopy Method. Nature Methods. Submitted.
• P. P. Mondal, G. Vicidomini, and A. Diaspro. A Unifying Image Reconstruction Methodology for Confocal-, Two Photon Excitation- and 4PI- Microscopy. Applied Physics Letters. Submitted.
• V. Caorsi, E. Ronzitti, G. Vicidomini, S. Krol, G. McConnell, and A. Diaspro. 2007. FRET measurements on fuzzy fluorescent nanostructures. Microscopy Research and Technique 70:452-458.
• G. Colombetti, G. Checcucci, S. Lucia, C. Usai, P. Ramoino, P. Bianchini, M. Pesce, G. Vicidomini, and A. Diaspro. 2007. Evidence for ciliary pigment localization in colored ciliates and implications for their photosensory transduction chain. A confocal microscopy study. Microscopy Research and Technique. 70:1028-1033.
• D. Mazza, F. Cella, G. Vicidomini, S. Krol and A. Diaspro. 2007. Role of three-dimensional bleach distribution in confocal and two-photon fluorescence recovery after photobleaching experiments. Applied Optics. 46(30):7401-7411.
• P. P. Mondal, G. Vicidomini, and A. Diaspro. 2007. Markov random field aided Bayesian approach for image reconstruction in confocal microscopy. Journal of Applied Physics. 102:044701.
• G. Vicidomini, M. Schneider, P. Bianchini, S. Krol, T. Szellas and A. Diaspro. 2007. Characterization of uniform ultra-thin layer for z-response measurements in 3D section fluorescence microscopy. Journal of Microscopy. 225:88-95.
• G. Vicidomini, P. P. Mondal and A. Diaspro. 2006. Fuzzy logic and maximum a-posteriori based image restoration for confocal microscopy. Optics Letters. 31(24):3582-3584.
• A. Diaspro, P. Bianchini, G. Vicidomini, M. Faretta, P. Ramoino, and C. Usai. 2006. Multi-photon excitation microscopy. BioMedical Engineering OnLine. 5:36.
• P. Bonetto, P. Boccacci, M. Scarito, M. Davolio, M. Epifani, G. Vicidomini , C. Tacchetti, P. Ramoino, C. Usai, and A. Diaspro. 2004. Three-Dimensional Microscopy Migrates to the Web With "PowerUp Your Microscope". Microscopy Research and Technique. 64(2):196-203.
• F. Difato, F. Mazzone, S. Scaglione, M. Fato, F. Beltrame, L. Kubìnovà, J. Janàcek, P. Ramoino, G. Vicidomini , and A. Diaspro. 2004. Improvemente in volume Estimation From Confocal Sections after Image Deconvolution. Microscopy Research and Technique. 64(2):151-155.

Book Chapters

• A. Diaspro, M.Schneider, P. Bianchini, V. Caorsi, D. Mazza, M. Pesce, I. Testa, G. Vicidomini, and C. Usai. 2006. Two-Photon Excitation Fluorescence Microscopy. In Science of  Microscopy. P.W. Hawkes, J. C. H Spence, editors. Vol. 2: 751–789. Springer, New York.

Conference Proceedings

• A. Diaspro, I. Testa, M. Faretta, R. Magrassi, S. Barozzi, D. Parazzoli, G. Vicidomini. 2006. 3D localized photoactivation of pa-GFP in living cells using two-photon interactions, in Engineering in Medicine and Biology Society, 28th Annual International Conference , Proceedings of IEEE-EMBS Vol. 1:389-391
• G. Vicidomini, P. P. Mondal and A. Diaspro. 2006. Soft computing approach to confocal and two-photon excitation microscopy, in Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIV, Jose-Angel Conchello, Carol J. Cogswell, Tony Wilson, Editors, Proceedings of SPIE Vol. 6443:644319.
• G. Vicidomini, J. Zwier, P. Bianchini, F. Cella, E. Ronzitti, S. Krol, T. Szellas, F. Brakenoff and A. Diaspro. 2007. SIPcharts using uniform ultra-thin and thin layers for z-response measurements in two-photon excitation fluorescence microscopy, in Multiphoton Microscopy in the Biomedical Sciences VII, Ammasi Periasamy,  Peter T.C. So, Editors, Proceedings of SPIE Vol.  6442:644224.
• M. Bertero, P. Boccacci, G. Desiderà and G. Vicidomini. 2006. High-resolution nimaging by multiple-image deconvolution, in Information Optics: 5th International Workshop on Information Optics, Gabriel Cristobal, Bahram Javidi, Santiago Vallmitjana, Editors, Proceedings of AVI Conferences Vol. 860:3-14.
• I. Testa, S. Barozzi, G. Vicidomini,D. Parazzoli, M. Faretta and A. Diaspro. 2006. T2P-GFP: two-photon photoactivation of PA-GFP in the 720-840 nm spectral region, in Multiphoton Microscopy in the Biomedical Sciences VI, Ammasi Periasamy, Peter T.C. So, Editors, Proceedings of SPIE Vol. 6089:175-184.
• A. Diaspro, P. Bianchini, V. Caorsi, D. Mazza, M. Pesce, I. Testa, G. Vicidomini, G. Chirico, F. Cannone and C. Usai. 2005. From Microscopy to Nanoscopy: How to Get and Read Optical Data at Single Molecule Level Using Confocal and Two-Photon Excitation Micriscopy, in NATO Security Through Science, Subseries B: Physics and Biophysics. V. Evangelista, L. Barsanti, V. Passarelli, P. Gualtieri, Editors, Proceedings of From Cells to Proteins: Imaing Nature across Dimensions, Vol. 3:187-207.
• G. Vicidomini. 2005. Image Formation In Fluorescence Microscopy: Three-Dimensional Mathematical Model, in NATO Security Through Science, Subseries B: Physics and Biophysics. V. Evangelista, L. Barsanti, V. Passarelli, P. Gualtieri, Editors, Proceedings of From Cells to Proteins: Imaing Nature across Dimensions, Vol. 3:371-393.

Conferences, Seminars, Short Visits

• 3-6/12/2007 Genoa. (Italy)
  Microscopia: dalle molecole al paziente. Generare ed interpretare immagini in biomedicina. Invited Lesson: "Correlative light electron microscopy".
• 3-6/10/2007 Rome. (Italy)
  XXV Conferenza Nazionale di Citometria a Flusso. Oral Presentation: " High Throughput 3D correlative microscopy".
• 10-13/4/2007 Valencia. (Spain)
  Focus on Microscopy. Oral Presentation: "Markov random filed aided image restoration in confocal and two-photon excitation microscopy".
• 3-7/3/2007 Baltimora. (Maryland, USA)
  American Biophysical Society Annual Meeting. Poster Presentation: " High Throughput 3D correlative microscopy".
• 29/1-2/2/2007 Venice. (Italy)
  XI School of Pure and Applied Biophysics. Advanced optical microscopy methods in biophysics. Invited Lesson: "Imaging in 3D fluorescence microscopy".
• 20-25/1/2007 San Jose. (California, USA)
  SPIE Photonics West. Posters Presentation: "Soft computing approach to confocal and two-photon excitation microscopy" and "SIPcharts using uniform ultra-thin and thin layers for z-response measurements in two-photon excitation fluorescence microscopy".
• 18-21/9/2006 Palermo. (Italy)
  XVIII SIBPA (Società Italiana di Biofisica Pura e Applicata) Annual Meeting. Poster Presentation: "Utilization of uniform ultra-thin fluorescent layers to quantify the z-response of 3d optical microscopes".
• 9-12/3/2006 Pert. (Western Australia)
  Focus on Microscopy. Poster Presentation: "Nano-organized thin layer and SIPcharts representation".
• 18-22/2/2006 Salt Lake City.(Utah, USA)
  American Biophysical Society Annual Meeting.
• 21-24/11/2005 Genoa. (Italy)
  Introduzione alla microscopia in fluorescenza. Invited Lesson: "La deconvoluzione e il 3D imaging".
• 6-8/10/2005 San Benedetto del Tronto. (Italy)
  XXII Conferenza Nazionale di Citometria a Flusso. Poster Presentation:
  G. Vicidomini, M. Schneider, P. Bianchini, I. Testa, C. Usai, P. Boccacci and A. Diaspro. 2006. Improvement of resolution in three-dimensional fluorescence microscopy throught the web with Power-Up Your Microscope, in Abstract of XXII National Conference of the Italian Society of Cytometry. R. De Vita, G. Mazzini, Editors. Citometry 64(A), 470.
• 4-5/10/2005 San Benedetto del Tronto. (Italy)
  Scuola Nazionale di Citometria. Corsi residenziali di aggiornameto. Invited Lesson: "La deconvoluzione ed il miglioramento della qualità e dell’analisi quantitativa delle immagini microscopiche".
• 22-25/6/2005 Genoa. (Italy)
  MMD (Matter, Materials and Devices) Annual Meeting. Poster Presentation: "Co-localization Analysis after Deconvolution in Two-Photon Excitation Microscopy".
• 6-10/6/2005 Florence. (Italy)
  Corso di Perfezionamento in Microscopie Innovative per le Biotecnologie. Oral presentation: "Powermicroscope: deconvoluzione per singolo e doppio fotone".
• 20-23/3/2005 Jena. (Germany)
  Focus on Microscopy. Poster Presentation: "Improvement of Resolution of Three-Dimnsional Fluorescence Microscopy Through the Web with “Power-Up Your Microscope”.
• 12-16/2/2005 Long Beach. (California, USA)
  American Biophysical Society Annual Meeting.
• 22-25/9/2004 Pisa. (Italy)
  XVII SIBPA (Società Italiana di Biofisica Pura e Applicata) Annual Meeting. Poster Presentation: "3D image restoration using Point-Spread-Function modelling and Web-Based approach".
• 12-23/9/2004 Pisa. (Italy)
  From Cells To Proteins: Imaging Nature Across Dimensions. International School Sponsored by the N.A.T.O. Scientific Affairs Division. Oral Presentation: "Image deconvolution: application in microscopy".
• 14-16/7/2004 Genoa. (Italy) 
  Principles of Fluorescence Techniques Course. Edition II 
• 8-10/6/2004 Genoa. (Italy)
  INFM (Istituto Nazionale Fisica della Materia) Annual Meeting. Poster Presentation: "Three-dimensional Microscopy Image Analysus migrates to the Web at www.powermicroscope.com"

Annual Reports

• 2005.
  My intent in this first year was to enrich my background knowledge in restoration imaging and in 3D fluorescence microscopy. I studied the mathematical model of image formation in 3D fluorescence microscopy (Wide-Field, Confocal and Two-Photon-Excitation microscopy) and I started one preliminary work concerning the study of statistical approach algorithms. In particular I used the C language to implement the image formation model and the Expectation-Maximizzation (EM) alghoritm. During my first year I collaborated with Prof. Alberto Diaspro (LAMBS).
  
  
• 2006.
  The second year of my PhD has been devoted to the study of maximum a-posteriori image restoration approach to 3D confocal microscopy. This approach has the potential advantage of incorporation of prior knowledge in the reconstruction process through the prior function. The image field is suitably modeled as a Markov random field resulting in a Gibbs distribution for the prior function. This allows to model characteristics of an object, such as local smoothness or edge, in terms of potential functions. A fuzzy-logic-based potential is employed in the Gibbs prior. Unlike other potentials, the fuzzy potential distinguishes intensity variation due to genuine edges and noise. The proposed approach has generated artifact-free restored confocal microscopy images. Also During this second year I collaborated with Prof. Alberto Diaspro (LAMBS).
  
  
• 2007.
  In the third year of my PhD I continued to explore the combination of Markov random field (MRF) and maximum a-posteriori approach for the solution of the regularized 3D fluorescence microscopy image restoration problem. A new wide class of non-quadratic potential functions, specially designed for edge-preserving image restoration, are studied and tested both on simulated and on real data-sets. Moreover, a new general approach, called split gradient method (SGM), is extended to the 3D fluorescence microscopy case, and integrated with the MRF approach to produce suitable iterative methods for the solution of the regularized image restoration problem. Also during this third year I collaborated with Prof. Alberto Diaspro (LAMBS).