Salk Institute
Waitt Advanced Biophotonics Center
Axel  Nimmerjahn

Axel Nimmerjahn

Assistant Professor
Waitt Advanced Biophotonics Center

The human brain consists of sets of cells that form networks of dazzling complexity. Much research has focused on understanding the circuits formed by neurons, the electrically-excitable cells that process and transmit information. However, glial cells, the second major cell type in the brain, account for about ninety percent of human brain cells and more than fifty percent of the brain's volume. For a long time, these cells were believed to have a merely passive, supportive role. However, over the past few years, it has become clear that glial cells make crucial contributions to the formation, operation and adaptation of neural circuitry.

Work in my lab is centered on innovating light microscopic tools that enable the study of these electrically largely non-excitable cells and their interaction with other cells in the intact mammalian brain. We have created tools for cell-type-specific staining and genetic manipulation, for imaging cellular dynamics in awake behaving mammals and for automated analysis of large-scale imaging data. This allows us to directly address longstanding questions regarding glial function in the intact healthy and diseased brain. Resolving these fundamental questions has broad implications for our view of glial cells, the way information is processed in the brain, the interpretation of functional brain imaging signals and the treatment of neurodegenerative brain disease.


  • MS, Physics, Max Planck Institute for Medical Research/University of Heidelberg, Germany
  • PhD, Physics, Max Planck Institute for Medical Research/University of Heidelberg, Germany
  • Postdoctoral Fellow, Biology and Applied Physics, Stanford University, U.S.A.

Awards and Honors

  • National Institutes of Health (NIH) Exceptional Unconventional Research Enabling Knowledge Acceleration (EUREKA) Award, 2013-2017
  • National Institutes of Health (NIH) Director's New Innovator Award, 2012-2017
  • Whitehall Foundation Award, 2011-2014
  • Rita Allen Scholar Award, 2011-2016
  • Human Frontiers Science Program (HFSP) Postdoctoral Fellowship, 2006-2009
  • Feodor Lynen Research Fellowship of the Alexander von Humboldt Foundation, 2006
  • Otto-Hahn-Medal and -Award of the Max Planck Society, 2006
  • Du Bois-Reymond Award of the German Physiologic Society, 2006
  • Böhringer Ingelheim Fonds (B.I.F.) Predoctoral Fellowship, 2002-2005

Selected Publications

  • Knowland, D., Arac, A., Sekiguchi, K.J., Hsu, M., Lutz, S.E., Perrino, J., Steinberg, G.K., Barres, B.A., Nimmerjahn, A.*, and Agalliu, D.* (2014). Stepwise recruitment of transcellular and paracellular pathways underlies blood-brain barrier breakdown in stroke. Neuron, in press. *Authors contributed equally [Link to article]
  • Ghosh, K.K., Burns, L.D., Cocker, E.D., Nimmerjahn, A., Ziv, Y., Gamal, A.E., and Schnitzer, M.J. (2011). Miniaturized integration of a fluorescence microscope. Nature Methods 8, 871-878.
  • Nimmerjahn, A., Mukamel, E.A., and Schnitzer, M.J. (2009). Motor behavior activates Bergmann glial networks. Neuron 62, 400-412.
  • Mukamel, E.A., Nimmerjahn, A., and Schnitzer, M.J. (2009). Automated analysis of cellular signals from large-scale calcium-imaging data. Neuron 63, 747-760.
  • Flusberg, B.A.*, Nimmerjahn, A.*, Cocker, E.D.*, Mukamel, E.A., Barretto, R.P.J., Ko, T.H., Burns, L.D., Jung, J.C., and Schnitzer, M.J. (2008). High-speed, miniaturized fluorescence microscopy in freely moving mice. Nature Methods 5, 935-938. *Authors contributed equally
  • Nimmerjahn, A., Kirchhoff, F., and Helmchen, F. (2005). Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo. Science 308, 1314-1318.
  • Nimmerjahn, A., Kirchhoff, F., Kerr, J.N.D., and Helmchen, F. (2004). Sulforhodamine 101 as a specific marker of astroglia in the neocortex in vivo. Nature Methods 1, 31-37.
  • Dittgen, T., Nimmerjahn, A., Komai, S., Licznerski, P., Waters, J., Margrie, T.W., Helmchen, F., Denk, W., Brecht, M., and Osten, P. (2004). Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo. Proc. Natl. Acad. Sci. USA 101, 18206-18211.
  • For a complete listing of publications on PubMed, click here>>

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