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Axel Nimmerjahn, PhD

Axel Nimmerjahn, PhD

Assistant Professor

Contact Information

Salk Institute for Biological Studies
10010 N. Torrey Pines Road
La Jolla, CA 92037
Office Tel: 858-453-4100 ext. 1063
Lab Website:

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.

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.