Matt Joens

Transmission, Scanning Electron and Focussed Ion Beam Microscopy
Staff Scientist, WUCCI

As a Staff Scientist in the WUCCI, Matthew’s primary responsibility is the preparation of cell and tissue samples for imaging using transmission and scanning electron microscopy methods, as well as the development of new cryo-preparation and correlative light and electron microscopic techniques. His background also includes extensive experience with high pressure freezing, immunolabeling, and 3D electron microscopy, including electron tomography, serial section reconstructions, and serial blockface imaging.

Matthew is an analytical chemist by undergraduate training and has over 8 years of electron microscope experience. His introduction into microscopy included internships at the University of California – San Diego (UCSD) with Dr. Timothy Baker, who is one of the founding fathers of cryo-electron microscopy, and with the National Center for Microscopy Imaging Research (NCMIR), a NIH funded lab headed by Dr. Mark Ellisman. Following these internships, he moved to the Salk Institute for Biological Studies where he worked with Dr. James Fitzpatrick to establish and grow the electron microscopy division of the Waitt Advanced Biophotonics Center.


  • B.S. in Analytical Chemistry, UC San Diego, CA, USA

Selected Publications

  • C.-C. Shih, D.M. Oakley, M.S. Joens, R.A. Roth and J.A.J. Fitzpatrick. 2017. Chapter 3: Non-Linear Optical Imaging of Extracellular Matrix Proteins. Methods in Cell Biology. In press.
  • J.N. Walker, A.L. Flores-Mireles, C.L. Pinker, H.L Schreiber, M.S. Joens, A.M. Park, A.M. Potretzke, J.S. Pinker, J.A.J. Fitzpatrick, A.Desai, M.G. Caparon and S.J. Hultgren. 2017. Catheterization alters the bladder ecology to potentiate Staphylococcus aureus infection of the urinary tract. PNAS. In press.
  • H.G. Lo, R.U. Jin, G. Sibbel, D. Liu, A. Karki, M.S. Joens, Blair B. Madison, B. Zhang, V. Blanc, J.A.J. Fitzpatrick, N.O. Davidson, S.F. Konieczny and J.C. Mills. 2016. A single transcription factor is sufficient to induce and maintain secretory cell architecture. Genes and Development. 31 (2), 154-171
  • J.D. Woodson, M.S. Joens, A.B. Sinson, J.Gilkerson, P.A. Salone, D. Weigel, J.A.J. Fitzpatrick and J. Chory. 2015. Ubiquitin facilitates a quality control pathway that removes damaged chloroplasts. Science. 350(6259), 450-454.
  • B.E. Kerman, H.J. Kim, K. Padmanabhan, A. Mei, S. Georges, M.S. Joens, J.A. J. Fitzpatrick, R. Jappelli, K.J. Chandross, P. August, and F.H. Gage. 2015. In vitro myelin formation using embryonic stem cells Development. Jun;142(12):2213-25.
  • M.W. Adams, A.F. Loftus, S.E. Dunn, M.S. Joens and J.A.J. Fitzpatrick. 2015. Invited Chapter on "Light-Sheet Fluorescence Microscopy". Current Protocols in Cytometry. 71:12.37.1-12.37.15.
  • H. Contreras, M.S. Joens, L.M. McMath, V.P. Le, M.V. Tullius, J.M. Kimmey, N. Bionghi, M.A. Horwitz, J.A.J. Fitzpatrick and C.W. Goulding. 2014. Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins. Journal of Biological Chemistry, May 22 pii: jbc.M114.570119.
  • M.S. Joens, C. Huynh, J.M. Kasuboski, D. Ferranti, Y.J. Sigal, F. Zeitvogel, M. Obst, C.J. Burkhardt, K.P. Curran, S.H. Chalasani, L.A. Stern, B. Goetze and J.A.J. Fitzpatrick. 2013. Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution. Scientific Reports, 3, 3514.
  • Y.H. Chien, M.E. Werner, J. Stubbs, M.S. Joens, J. Li, S. Chien, J.A.J. Fitzpatrick, B.J. Mitchell and C. Kintner. 2013. Bbof1 is required to maintain cilia orientation. Development. Aug;140(16):3468-77.
  • J.M. Kasuboski, Y.J. Sigal, M.S. Joens, B.F. Lillemeier and J.A.J. Fitzpatrick. 2012. Invited Chapter on "Super-Resolution Microscopy: a comparative treatment" Current Protocols in Cytometry. Oct; Chapter 2: Unit 2.17.
  • M. Hatori, C. Vollmers, A. Zarrinpar, L. Ditacchio, E.A. Bushong, S. Gill, M. Leblanc, A. Chaix, M.S. Joens, J.A.J. Fitzpatrick, M.H. Ellisman and S. Panda. 2012. Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metabolism. Jun 6; 15(6):848-60.