Please note that there was no lab corresponding to lectures 1, 12, 14, and 15.

1 Course Introduction; Overview of Neurotechnology Refresh your memory of the concepts of diffraction-limited resolution, point spread function, combining tube lenses and objective lenses, and fluorescence excitation and emission at Nikon's MicroscopyU.

Advanced Microscopy

Guest lecturers: Prof. Elly Nedivi, Prof. Peter So

Chen, Jerry L., Walter C. Lin, et al. "Structural Basis for the Role of Inhibition in Facilitating Adult Brain Plasticity." Nature Neuroscience 14, no. 5 (2011): 587–94.

Chen, Jerry L., Katherine L. Villa, et al. "Clustered Dynamics of Inhibitory Synapses and Dendritic Spines in the Adult Neocortex." Neuron 74, no. 2 (2012): 361–73.

So, Peter T. C., Chen Y. Dong, et al. "Two-photon Excitation Fluorescence Microscopy." Annual Review of Biomedical Engineering 2, no. 1 (2000): 399–429.

So, Peter T. C., Elijah Y. S. Yew, et al. "High-throughput Nonlinear Optical Microscopy." Biophysical Journal 105, no. 12 (2013): 2641–54.

Lab 2

Advanced Microscopy Imaging

Guest Lecturer: Kalen Berry, Elijah Yew


High-density Electrophysiology

Guest lecturer: Prof. Matt Wilson

Brown, Emery N., Robert E. Kass, et al. "Multiple Neural Spike Train Data Analysis: State-of-the-art and Future Challenges." Nature Neuroscience 7, no. 5 (2004): 456–61.

Buzsáki, György, Costas A. Anastassiou, et al. "The Origin of Extracellular Fields and Currents—EEG, ECoG, LFP and Spikes." Nature Reviews Neuroscience 13, no. 6 (2012): 407–20.

Womelsdorf, Thilo, Jan-Mathijs Schoffelen, et al. "Modulation of Neuronal Interactions through Neuronal Synchronization." Science 316, no. 5831 (2007): 1609–12.

Lab 3

Digital Electrophysiology

Guest Lecturer: Jon Newman


Microfluidics and Cell Engineering

Guest Lecturers: Prof. Roger Kamm & Sebastien Uzel

Kothapalli, Chandrasekhar R., Ed van Veen, et al. "A High-throughput Microfluidic Assay to Study Neurite Response to Growth Factor Gradients." Lab on a Chip 11, no. 3 (2011): 497–507.

Park, Jae Woo, Hyung Joon Kim, et al. "Advances in Microfluidics-based Experimental Methods for Neuroscience Research." Lab on a Chip 13, no. 4 (2013): 509–21.

Shin, Yoojin, Sewoon Han, et al. "Microfluidic Assay for Simultaneous Culture of Multiple Cell Types on Surfaces or within Hydrogels." Nature Protocols 7, no. 7 (2012): 1247–59.

Lab 4 Microfluidics and Cell Engineering (cont.)  

EM-based Connectomics

Guest Lecturer: Dr. Daniel Berger

Lichtman, Jeff W., and Winfried Denk. "The Big and The Small: Challenges of Imaging the Brain's Circuits." Science 334, no. 6056 (2011): 618–23.

Briggman, Kevin L., and Davi D. Bock. "Volume Electron Microscopy for Neuronal Circuit Reconstruction." Current Opinion in Neurobiology 22, no. 1 (2012): 154–61.

Marx, Vivien. "Neurobiology: Brain Mapping in High Resolution." Nature 503, no. 7474 (2013): 147–52.

Tomassy, Giulio Srubek, Daniel R. Berger, et al. "Distinct Profiles of Myelin Distribution along Single Axons of Pyramidal Neurons in the Neocortex." Science 344, no. 6181 (2014): 319–24.

Lab 5

EM-based Connectomics (cont.)

Field Trip: Lichtman lab at Harvard

6 Optogenetics

Kodandaramaiah, Suhasa B., Giovanni Talei Franzesi, et al. "Automated Whole-cell Patch-clamp Electrophysiology of Neurons in Vivo." Nature Methods 9, no. 6 (2012): 585–87.

Klapoetke, Nathan C., Yasunobu Murata, et al. "Independent Optical Excitation of Distinct Neural Populations." Nature Methods 11, no. 3 (2014): 338–46.

Chuong, Amy S., Mitra L. Miri, et al. "Noninvasive Optical Inhibition with a Red-shifted Microbial Rhodopsin." Nature Neuroscience 17, no. 8 (2014): 1123–29.

Prevedel, Robert, Young-Gyu Yoon, et al. "Simultaneous Whole-Animal 3D Imaging of Neuronal Activity Using Light-field Microscopy." Nature Methods 11, no. 7 (2014): 727–30.

Lab 6a Optogenetics (cont.)  
Lab 6b Auto Patch Clamping  
7 & Lab

Virus Engineering

Guest Lecturer: Dr. Ian Wickersham

Atasoy, Deniz, Yexica Aponte, et al. "A FLEX Switch Targets Channelrhodopsin-2 to Multiple Cell Types for Imaging and Long-range Circuit Mapping." The Journal of Neuroscience 28, no. 28 (2008): 7025–30.

Wickersham, Ian R., David C. Lyon, et al. "Monosynaptic Restriction of Transsynaptic Tracing from Single, Genetically Targeted Neurons." Neuron 53, no. 5 (2007): 639–47.


Magnetoencephalography (MEG)

Guest Lecturer: Prof. Dimitrios Pantazis

Cichy, Radoslaw Martin, Dimitrios Pantazis, et al. "Resolving Human Object Recognition in Space and Time." Nature Neuroscience 17, no. 3 (2014): 455–62.

Baillet, Sylvain, John C. Mosher, et al. This resource may not render correctly in a screen reader."Electromagnetic Brain Mapping." (PDF) IEEE Signal Processing Magazine 18, no. 6 (2001): 14–30.

Lab 8 MEG (cont.)  

Structural Magnetic Resonance Imaging (MRI)

Guest Lecturer: Dr. Atsushi Takahashi

Buy at MIT Press Amazon logo Raichle, Marcus E. "Functional Neuroimaging: A Historical and Physiological Perspective." In Handbook of Functional Neuroimaging of Cognition. MIT press, 2001, pp. 3–26. ISBN: 9780262032803.

Amazon logo Huettel, Scott A., Allen W. Song, and Gregory McCarthy. Functional Magnetic Resonance Imaging. Vol. 1. Sinauer Associates, 2004. ISBN: 9780878932887.

Mesulam, Marsel. "The Evolving Landscape of Human Cortical Connectivity: Facts and Inferences." Neuroimage 62, no. 4 (2012): 2182–89.

Lab 9 Structural MRI  

Functional and Molecular MRI

Guest Lecturer: Dr. Atsushi Takahashi

Lab 10 Functional and Molecular MRI (cont.)  

High Throughput Neuroscience

Guest Lecturer: Dr. Limor Freifeld

Grewe, Benjamin F., and Fritjof Helmchen. "Optical Probing of Neuronal Ensemble Activity." Current Opinion in Neurobiology 19, no. 5 (2009): 520–29.

Looger, Loren L., and Oliver Griesbeck. "Genetically Encoded Neural Activity Indicators." Current Opinion in Neurobiology 22, no. 1 (2012): 18–23.

Lemon, William C., and Philipp J. Keller. "Live Imaging of Nervous System Development and Function using Light‐sheet Microscopy." Molecular Reproduction and Development (2013).

Lab 11 High Throughput Neuroscience Yanik Lab  
12 Discussion of Final Project Guidelines  

Whole-brain Optical Imaging

Guest Lecturer: Prof. Kwanghun Chung

Chung, Kwanghun, Jenelle Wallace, et al. "Structural and Molecular Interrogation of Intact Biological Systems." Nature 497, no. 7449 (2013): 332–37.
Lab 13 CLARITY  
14 Final Presentations I  
15 Final Presentations II