Kim TH, Zhang Y, Lecoq J, Jung JC, Li J, Zeng H, Niell CM, Schnitzer MJ. (2016) Long-Term Optical Access to an Estimated One Million Neurons in the Live Mouse Cortex. Cell Rep. 17(12):3385-3394.

• Movie S1. Epi-fluorescence Ca2+ Imaging through the Crystal Skull across the Cortex of a GCaMP6f-tTA-dCre Transgenic Mouse Reveals Neuropil and Single-Cell Ca2+ Activity.


• Movie S2. Epi-fluorescence Ca2+ Imaging through the Crystal Skull over the Retrospenial Area of a GCaMP6f-tTA-dCre Transgenic Mouse Reveals both Neuropil and Single-Cell Ca2+ Activity.


• Movie S3. Epi-fluorescence Video of Ca2+ Activity in the Same Mouse as in Movie S2, but Acquired 3 Weeks Later, at 11 Weeks after Implantation of the Curved Glass Window.

MJS Presentation at the Brain 2016 Forum, Lausanne, Switzerland.

• Imaging large scale ensemble neural codes underlying learning and memory, Prof Mark Schnitzer.

NeuroPod, June, 2015.

• Episodic exploration: Short-lived synapses explain the duration of episodic memory retention in the hippocampus (Research paper: Attardo et al.).

Savall J, Ho ET, Huang C, Maxey JR, Schnitzer MJ. (2015) Dexterous robotic manipulation of alert adult Drosophila for high-content experimentation. Nat Methods. 12(7):657-60.[Link]

• Video 1: The robot tracks and captures a fly under infrared illumination using real-time machine vision guidance. Automated tracking and picking of an active fly from the picking platform, played back at real speed.


• Video 4: The robot captures three flies and transfers them to head holders. After picking each fly, the robot carried it to an inspection camera and obtained the location of the neck apse. The robot used this information to align and tether the head of the fly to the holder. Since the head holders were based on suction, we released all three flies after the experiment.


• Video 6: Rapid robotic manipulation of alert flies The robot rapidly transfers flies back and forth between the halves of a divided platform. This demonstration illustrates high-speed handling of flies.


• Video 9: The robot holds a fly as it walks on an air-suspended ball for studies of odor-evoked locomotion. We recorded the forward, lateral, and rotational components of the locomotor patterns in response to odor stimuli, which we delivered through the pipette directed toward the fly's head.


• Video 10: Mechanical microsurgery of the fly cuticle, to expose the brain for in vivo imaging. Using a three-dimensional translation stage, we maneuvered the head-fixed fly to the end mill and made an initial cut to open the cuticle. Thereafter, we commanded the stage to continue cutting along a preprogrammed trajectory. Saline immersion kept the brain hydrated and prevented tissue debris from interfering with the surgery.

Milken Institute Global Conference.

• Unlocking the Mysteries of the Brain. (1 hr)

The White House Conference on the BRAIN Initiative.

• The White House Conference on the BRAIN Initiative. (1 hr 28 min)

iBiology Microscopy Course, Specialized Microscopy Lecture.[ibiology.org]

• Miniature Microscopes for Deep Tissue Imaging. (38 min)

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. 16(3):264-6.[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]

• Mouse behavior and microcirculation in the cerebellar vermis recorded concurrently in a mouse with an integrated microscope mounted on the cranium.

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]

• Three-dimensional image stack of hippocampal blood vessels acquired in a live mouse by two-photon microendoscopy and intravascular injection of fluorescein-dextran.


• Hippocampal microcirculation in normal tissue imaged by high-speed one-photon microendoscopy and intravascular injection of fluorescein-dextran.


• High-speed imaging of microcirculation in a hippocampal glioma using one-photon microendoscopy.

Stanford News August 27, 2009

• CNC: A new neuroscience program at Stanford co-directed by Mark J. Schnitzer and Karl Deisseroth

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]

• A three-dimensional stack of images acquired by second-harmonic microendoscopy from the lateral gastrocnemius muscle of a living mouse. A 1-mm-diameter microendoscope placed on top of the muscle was used to create an image stack extending 135 µm in depth and containing 270 images acquired at 0.5 µm increments. The imaging parameters and optical arrangement were the same as in all other animal imaging experiments (Methods). The white scale bar indicates 50 µm.

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]

• Voltage trace (A) and phase plane trajectory (B) of a rebound depolarization driven by a conditioned stimulus (CS) in a model deep cerebellar nuclei (DCN) neuron , following classical eyeblink conditioning with a long interstimulus interval (ISI) of 190 ms. At the start of the CS, increased spiking by Purkinje cells hyperpolarizes the DCN cell and deinactivates T-type channels. About 35 ms prior to the time of the expected US, release of the hyperpolarizing drive leads to a rebound depolarization.
  
  
• Voltage trace (A) and phase plane trajectory (B) of a rebound depolarization driven by a conditioned stimulus in a model DCN neuron, following training with a short interstimulus interval (ISI) of 85 ms. Due to the short ISI, the rebound amplitude is diminished and the phase plane trajectory does not move as far into the reliable retrieval zone (red shading) as with a long ISI value.
  
  
• Voltage trace (A) and phase plane trajectory (B) of a rebound depolarization driven by a conditioned stimulus in a model DCN neuron, following training with an intermediate interstimulus int erval (ISI) of 90 ms. The stochastic arrival times of synaptic inputs leads to variations in the voltage dynamics between the 20 traces shown, despite identical initial conditions at t = -100 ms (red and blue traces). This ISI value leads to unreliable retrieval of the stored memory. Noisy synaptic inputs lead some phase plane trajectories (red dots) closer to the reliable retrieval zone (warm colors in color map) and toward a higher level of deinactivation of T-type Ca2+ channels, while other trajectories are more distant from the reliable retrieval zone (blue dots).

You need Quicktime or a compatible movie player to view these movies (.mov format).

ABC News visits the Schnitzer Lab Oct. 19, 2007.

• Stanford Scientist Among 'Brilliant 10' For Creating A Microscope That 'Reads Minds'

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

• Miniature microscope creates micron-sized images of capillaries in live animals.

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]

• Live image from the CA1 hippocampal area of a live mouse. This is an example of a "to-and-fro" flow pattern. (Quicktime)
  
  
• Live image from CA1 hippocampus of a live rat. (Quicktime)
  
  
• Live image from the laterodorsal thalamic nucleus of a live rat. (Quicktime)