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Nanoscopy & NIC@IIT


IIT Central Research Lab Genova


Via Morego 30, Genova
+39 010 71781 320

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Francesca Cella Zanacchi is currently a researcher at the IItalian Institute of Technology in Italy in the Nanophysics department. Previously, she worked as a Postdoc at the Institute de Ciències Fotòniques (ICFO) in Spain and as post-doctoral fellow in the Nanoscopy group at the Italian Institute of Technology. She graduated in Physics at the University of Genoa (Italy) in 2006 and in 2010 she accomplished her PhD studies in Physics (University of Genoa). She was a visitor scientist at EMBL (Heidelberg) in 2008 and at University of Maine (USA) in 2009. In December 2013 she joined the Single Molecule Biophysics group at University of Frankfurt as a short term EMBO fellowship. She works in the bioengineering/biophysics field and her research activity is focused on the design, realization and utilization of optical imaging techniques to study biomolecules at the molecular level in thick biological samples and tissues. Her work is mainly  addressed to the study of biological molecules to investigate cell functioning using super-resolution microscopy, single molecule localization techniques (PALM, GSDIM), single molecule tracking, single plane illumination microscopy (SPIM), confocal, multiphoton fluorescence microscopy, nanostructured model systems and advanced fluorescence microscopy techniques (FRAP). She worked as a working package leader for the RENVISION European project (FP7-ICT-2011-9 (NBIS) # 600847) and she is active as member of several scientific societies and as reviewer for several international scientific journals. 

Past experience:

October 2016-current                  Researcher at Nanophysics Dept. of the Istituto Italiano di Tecnologia (IIT).

February 2017-May 2017               EMBO Short term fellowship (n. ASTF432-2016) at Biophysics Institute, Italian National Research Council (CNR)

May 2015-October 2016:             Post Doc at the Institute of Photonics Sciences, Barcelona, Spain. Tutor Melike Lakadamyali, Project:"DNA origami as versatile calibration standard for quantitative single molecules localization techniques".

July 2014- May2015                    Researcher at Nanophysics Dept. of the Istituto Italiano di Tecnologia (IIT).

Dec 2013-Feb 2014                     EMBO Short term fellowship at University of Frankfurt, Germany. Tutor: Mike Heilemann. Project: "Advanced super-resolution and 3D tracking techniques for   transcription studies in bacteria".

2010-July 2014                            Post Doc at Nanophysics Dept (Nanoscopy group) of the Istituto Italiano di Tecnologia (IIT),Genova, Italy. Tutor: A Diaspro. Project: "Advanced light sheet based fluorescence microscopy techniques".

Aug 2009 –Dec 2009                   Visiting research associate at University of Maine, Orono, Maine   Tutor: S. Hess. "Development of a fluorescence single molecule localization localization microscope   (FPALM) based on inclined illumination"

Aug 2008 –Dec 2008                   Visiting scientist at "Light Microscopy Group"- EMBL Heidelberg, Germany Tutor: E.H.K. Stelzer. "Selective plane microscopy in scattering samples"



2007-2009          Ph.D. Degree in Physics, Department of Physics, University of Genoa, Italy


2006                     MSc. Degree  in Physics, Department of Physics, University of Genoa, Italy


International/national  Prizes and Awards:

2018                                   SIBPA Award for Biophysical society meeting 2018 (San Francisco)

2013                                   International travel award - Biophysical society meeting 2013 (Phyladelphia)

2012                                   TR35-Giovani Innovatori Ed.2012

2012                                   NEST Prize per la Nanoscienza Ed. 2012

2011                                   Best poster award at BIOS 2011 SPIE Photonics West (SF)   

2006                                    Prize for Degree Thesis in Physics: Premio di Studio GIC (Società Italiana Citometria) Menzione  Speciale per  la tesi di Laurea intitolata “Ruolo dei profili di                                                   eccitazione nello studio della diffusione di molecole fluorescenti” .

Activity within European projects: 

Working Package leader within the EU project RENVISION (Retina-inspired ENcoding for advanced VISION tasks) awarded within the initiative of Future Emerging Technologies: Neuro-Bio-Inspired Systems (NBIS).


Patent submitted:

Reference no: EP17382394.9 "Method for quantifying protein copy number" 



 Main research projects:

  • 3D super-resolution imaging techniques based on light sheet microscopy for thick biological samples
  • Novel approaches for quantitative single molecule localization based on DNA nanotechnologies (DNA origami)
  • Quantitative studies at the synaptic level using single molecule localization techniques: from cells to tissues


Selected Publications


Selected  publications: 

  1. F. Cella Zanacchi*C. Manzo, A. Sandoval Alvarez, N. D. Derr, M. Garcia Parajo, M. Lakadamyali “A DNA Origami platform for quantifying protein copy-number in super-resolution Nature Methods 10.1038/nmeth.4342 (2017)

  2. Deschout H., Cella Zanacchi F., Mlodzianoski M., Diaspro A., Bewersdorf J., Hess S.T. & Braeckmans K., “Precisely and accurately localizing single emitters in fluorescence microscopyNature Methods 11, doi:10.1038/nmeth.2843 (2014).
  3. Cella Zanacchi F, Lavagnino Z., Perrone Donnorso M., Del Bue A., Furia L., Faretta M., Diaspro A. "Live-cell 3D superresolution imaging in thick biological samplesNature Methods. 8 (12):  DOI:10.1038/nmeth.1744 (2011).

  4. Francesca Pennacchietti, Sebastiano Vascon, Thierry Nieus, Christian Rosillo, Sabyasachi Das, Shiva Tyagarajan, Alberto Diaspro, Alessio del Bue, Enrica Maria Petrini, Andrea Barberis and Francesca Cella Zanacchi* "Nanoscale molecular reorganization of the inhibitory postsynaptic density is a determinant of GABAergic synaptic potentiation" Journal of Neuroscience,  0514-16; DOI: (2017)

  5. Z. Lavagnino, G. Sancataldo, M.d’Amora, P. Follert, D. De Pietri  Tonelli, A. Diaspro, F. Cella Zanacchi*, “4D (x-y-z-t) imaging of thick biological samples by means of Two Photon inverted Selective Plane Illumination Microscopy (2PE-iSPIM)Sci Reports 6, (2016) 

  6. G.Hilgen, M. Sorbaro, S. Pirmoradian, J. Muthmann, I. Edit Kepiro, S. Ullo, C. Juarez Ramirez, A.Puente Encinas, Al. Maccione, L. Berdondini, V. Murino, D. Sona, F. Cella Zanacchi, E. Sernagor, M. H.Hennig "Unsupervised spike sorting for large-scale, high-density multielectrode arrays", Cell reports, 18 (10), (2017)

  7. Lorén N., Hagman J., Jonasson J.K., Deschout H., Bernin D., Cella Zanacchi F., Diaspro A, McNally J.G., Ameloot M., Smisdom N., Nydén M., Hermansson H.M., Rudemo M. and Braeckmans K., “Fluorescence recovery after photobleaching in material and life sciences: putting theory into practice” Quarterly Reviews of Biophysics 48 (3), (2015)

  8. Cella Zanacchi F.* Lavagnino Z., Faretta M., Furia L., Diaspro A.,  "Light-sheet confined  super-resolution using two-photon photo-activation", Plos One 8 (7), oii:10.1371/journal.pone.0067667,(2013).

  9. A. Pierzyńska-Mach, A Szczurek, F. Cella Zanacchi, F. Pennacchietti, J. Drukała, A.Diaspro, C. Cremer, Z. Darzynkiewicz, J. W Dobrucki "Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopyCell Cycle 15 (8) ,(2016).

  10. Spahn C., Cella Zanacchi F., Ulrike Endesfelder U. and Heilemann M., “Correlative super-resolution imaging of RNA polymerase distribution and dynamics, bacterial membrane and chromosomal structure in Escherichia coli”, Methods and Applications in Fluorescence, Volume 3 (1), (2015) 

  11. Cella Zanacchi F.*, Bianchini P., Vicidomini G., "Fluorescence microscopy in the spotlight", Microscopy research and technique 77(7), 479-482 (2014)
  12. Lavagnino Z., Cella Zanacchi F.*, Ronzitti E., and Diaspro A. Two-photon excitation selective plane illumination microscopy (2PE-SPIM) of highly scattering samples: characterization and application Optics Express, Vol. 21, Issue 5, pp. 5998-6008 (2013)

  13. Chacko, J. V., Cella Zanacchi F. and Diaspro, A., "Probing cytoskeletal structures by coupling optical superresolution and AFM techniques for a correlative approachCytoskeleton 7(11), doi: 10.1002/cm.21139 (2013) 

  14. M. Perrone DonnorsoE. Miele, F. De Angelis, R. La Rocca, T. Limongi, F. Cella Zanacchi, S. Marras, R. Brescia and E. Di Fabrizio. Nanoporous Silicon Nanoparticles for drug delivery applications. Microelectronic Engineering. 2012.

  15. Mazza D., Braeckmans K., Cella F., Testa I., Vercauteren D., Demeester J., DeSmedt S.S., Diaspro A. . A new FRAP/FRAPa method for three-dimensional diffusion measurements based on multiphoton excitation microscopy. Biophys Journal 95(7), 3457–69 (2008)

  16. Cella Zanacchi F.Proc. of SPIE, vol.7903 “Multiphoton Microscopy in the Biomedical Sciences XI” "Two-photon fluorescence excitation within a light sheet based microscopy architecture" (2011)

  17. Cella F., Lavagnino Z., Diaspro A, Non-linear effects and role of scattering in multiphoton imaging of thick biological samples. Multiphoton Microscopy in the Biomedical Sciences IX Proceedings of the SPIE, Volume 7183, pp. 718324-718324-7 (2009)

  18. Cella F., Ronzitti E, Vicidomini G, Diaspro A, Studying the illumination puzzle towards an isotropic increase of optical Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XV (J.Conchello, C.J.Cogswell, T.Wilson, T.G.Brown) Proc. of SPIE Vol. 6861, 686112, (2008)



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I numeri di IIT

L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.

IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.

Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.

Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali

La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.

IIT: the numbers

Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance).  The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.

IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators110 researchers and technologists350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion  is 41% female against 59% male.

In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.

So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications12 up start-ups and as many  which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.