lab sculpture created by Steve Lohman


iBiology Microscopy Course, Specialized Microscopy Lecture.[]

Ziv Y, Burns LD, Cocker ED, Hamel EO, Ghosh KK, Kitch LJ, El Gamal A, and Schnitzer MJ. (2013) Long-term dynamics of CA1 hippocampal place codes. Nature Neuroscience. Epub ahead of print.[Link]

  • Ca2+-imaging in hundreds of CA1 pyramidal cells in a freely behaving mouse. A video showing a mouse exploring a circular arena (left panel) and the simultaneously acquired brain-imaging data of CA1 pyramidal cell Ca2+ activity, displayed as relative changes in fluorescence (deltaF/F) (right panel). 705 pyramidal cells were identified in the total data set and correspond to the neurons of Fig. 1b. The Ca2+-imaging frame rate was 20 Hz, but these data are shown down-sampled to 5 Hz to aid visualization of the Ca2+ transients. The video playback rate is sped up four-fold from how the events actually occurred.

Ghosh KK, Burns LD, Cocker ED, Nimmerjahn A, Ziv Y, Gamal AE, Schnitzer MJ. (2011) Miniaturized integration of a fluorescence microscope. Nat Methods. 8(10):871-8.[Link]

Barretto RP, Ko TH, Jung JC, Wang TJ, Capps G, Waters AC, Ziv Y, Attardo A, Recht L, Schnitzer MJ. (2011) Time-lapse imaging of disease progression in deep brain areas using fluorescence microendoscopy. Nat Med. 17(2):223-8.[Link]

Stanford News August 27, 2009

Nimmerjahn A, Mukamel EA, Schnitzer MJ. (2009) Motor behavior activates Bergmann glial networks. Neuron. 62(3):400-12. [Link]

  • Ca2+ Bursts Occur Spontaneously in Alert Resting Animals and Appear as a Radial Wave Expanding in Three Dimensions. A video clip taken from an 8 min recording acquired by three-dimensional (3D) two-photon microscopy in an awake, head-restrained mouse standing on the exercise ball, following injection of the cell membrane-permeant Ca2+-sensitive indicator OGB-1-AM into the cerebellar vermis. The video shows two examples of radially spreading bursts recorded in the cerebellar molecular layer across multiple optical planes at different depths below the pial surface. The planes shown range from 25-100 µm in depth spaced at 5 µm increments and were consecutively sampled at a rate of 49 ms per plane. The entire 3D stack was sampled at 1.1 Hz. Image data are displayed in a mosaic arrangement, with raw (left) and normalized (right) fluorescence signals. Normalized changes in fluorescence, deltaF(t)/F, were computed for each pixel as the difference between the instantaneous fluorescence, F(t), and the time-averaged fluorescence, F, divided by F. Elapsed time in seconds is shown in the upper right corner. Width of each individual image is 220 µm. Scale bar: 25 µm.

  • Ca2+ Flares are Triggered by Locomotion and Occur Across Areas Hundreds of Microns in Extent. This exemplary video taken from a 9.8 min recording in an awake head-restrained mouse shows Ca2+-activation in numerous Bergmann glial fibers across a 232 µm field of view before, during and after voluntary locomotor activity on an exercise ball. The time in seconds relative to movement onset is indicated in the upper right corner. Instantaneous running speed on the ball (in mm/s) as measured by the optical encoder is shown in the lower right corner. Fluorescence data were recorded in the cerebellar vermis by dual-color, two-photon microscopy following injection of the green fluorescent, cell membrane-permeant Ca2+-sensitive indicator OGB-1-AM (left) and topical application of the red fluorescent astrocyte marker SR101 (center). The right panel shows an overlay of the SR101 signals and normalized changes (deltaF(t)/F) in the OGB-1-AM signals, with the OGB-1-AM deltaF(t)/F signals represented in blue. Both primary glial fibers in the palisades highlighted by SR101 and the surrounding tissue areas participate in the Ca2+ flare. Virtually no motion artifacts are apparent, even when the mouse is running. The image acquisition rate was 20.35 frames per second, but to aid visualization of Ca2+-activation each frame in the movie shows an average of 10 consecutive frames. Scale bar, 25 µm.

Llewellyn ME, Barretto RPJ, Delp SL & Schnitzer MJ. (2008) Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans. Nature. 454 784-788. [Link]


Lock-and-key mechanisms of cerebellar memory recall based on rebound currents. Wetmore DZ, Mukamel EA, Schnitzer MJ. (2008) J Neurophysiol. 100:2328-2347. [Link]

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ABC News visits the Schnitzer Lab .

Fast-scanning two-photon fluorescence imaging based on a microelectromechanical systems two- dimensional scanning mirror. Piyawattanametha W, Barretto RP, Ko TH, Flusberg BA, Cocker ED, Ra H, Lee D, Solgaard O, Schnitzer MJ. (2006) Opt Lett. 31(13):2018-20. [Link]

  • MEMS Scanning. Movie showing a 750-micron square, silicon MEMS mirror as its inner and outer axes of scanned individually and then simultaneously

In vivo brain imaging using a portable 3.9 gram two-photon fluorescence microendoscope.
Flusberg BA, Jung JC, Cocker ED, Anderson EP, Schnitzer MJ. (2005) Opt Lett. 30(17):2272-4. [Link]

  • Device Mechanical Alignments. CAD movie of 3.9 gram fiberscope showing the coarse focusing, micromotor-controlled fine focusing, and fiber alignment capabilities.

  • Device "Explosion". CAD movie showing the construction of the 3.9 gram two-photon fluorescence fiberscope from its components.

  • Lissajous Scanning. Movie of 800 nm laser light exiting the tip of a photonic bandgap fiber as it is scanned in a Lissajous pattern.

Stanford News Sept. 2005

In vivo mammalian brain imaging using one- and two-photon fluorescence microendoscopy. Jung JC, Mehta AD, Aksay E, Stepnoski R, Schnitzer MJ. (2004). J Neurophysiol. 92(5):3121-33. [Link]