Neuroimaging Course

Advanced Neuroimaging Techniques

FEB 3 – FEB 15, 2020

This is an intensive and comprehensive laboratory-oriented course focusing on applying imaging techniques to neuroscience research. The objective of this imaging course is to gain exposure to modern imaging tools from the principles of optics to applications in modern neuroscience.

The course has been formatted to include lectures in the morning and laboratory sections in the afternoon and evening. Students will rotate through all laboratory sections, and focus on one section (and one optional section) for the remainder of the course.

Take a look inside MPFI’s Advanced Neuroimaging Course:


Laboratory Sections

Students will rotate through all laboratory sections and focus on one section for the remainder of the course.


Imaging deep brain structure with two-photon Microendoscope: Alessio Attardo, Ph.D.


  • Imaging CA1 neurons and Spines in live animals with the high NA GRIN lens in combination with 2-photon microscopy

  • Surgical preparation for deep brain imaging will be described and performed

Reference: Impermanence of dendritic spines in live adult CA1 hippocampus. Attardo A, Fitzgerald JE, Schnitzer MJ. Nature. 2015 Jun 22. doi: 10.1038/nature14467

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High resolution circuit mapping using temporal focused two-photon microscopy with CHR2 Activations: McLean Bolton, Ph.D.


  • Understand principle and setup of temporal focused two-photon microscopy

  • Use diffraction grating to control the lateral and axial profiles of a pulsed laser beam

  • Single cell resolution circuit mapping by temporal focused two-photon excitation in combination with novel spatially-restricted channel rhodopsin in brain slices

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Multiphoton photostimulation and imaging of neuronal populations in vivo: Valentina Emiliani, Ph.D.


  • Understand fundamental principles of two-photon imaging and two-photon photostimulation using holography and temporal focusing

  • Characterize properties of basic dual-function multiphoton microscope

  • Image neuronal activity and functional connectivity at the cellular resolution during simultaneous photostimulation of single cells and populations
  • Learn basics of image processing and analysis

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Long wavelength, 3-photon microscopy for in vivo deep brain imaging: Chris Xu, Ph.D.


  • Understand fundamental principles of deep imaging in scattering tissue

  • Learn and characterize properties of a 3-photon microscope.

  • Image neuronal structure and function at the cellular resolution deep in the mouse brain

  • Learn basics of signal-to-noise ratio and signal-to-background ratio in deep imaging

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Neural imaging in unrestrained animals: Kuan Hong Wang, Ph.D.


  • Understand basic principle of miniature microscope (miniscope) for in vivo Ca2+ imaging

  • Demonstrate surgical procedures for miniscope

  • Image neuronal activity and functional connectivity at the cellular resolution in freely-moving animals and process Ca2+ imaging data

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Two Photon Fluorescence lifetime imaging (FLIM) and fluorescence resonance energy transfer (FRET): Ryohei Yasuda, Ph.D.


  • Understand principle of FRET and FLIM.

  • Learn design principle of new FLIM-FRET sensors.

  • Image activity of proteins and protein-protein interaction in single dendritic spines in slice culture / in vivo using 2-photon FLIM.

  • Reference: H. Murakoshi, H. Wang, R. Yasuda. Localized, persistent activation of Rho GTPases during long-term structural plasticity induced in single dendritic spines. Nature, 472:100-4 (2011)

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In vivo imaging of structural plasticity in the mouse brain: Yi Zuo, Ph.D.


  • Understand principle and setup of 2-photon microscopy to visualize single dendritic spines in live animals.
  • Image structural plasticity of dendritic spines in live animals over days.
  • Demonstrate thin-scull and cranial window preparations.
  • Reference: Fu M, Yu X, Lu J and Zuo Y (2012) Repetitive motor learning induces coordinated formation of clustered dendritic spines in vivo. Nature 483(7387):92-95

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Electron Microscopy Module

CLEM (correlative light and electron microscopy) is a powerful technique that bridges the gap between functional fluorescence imaging and high resolution EM imaging. In this module, you will learn how to integrate different visualization workflows into your own project to tackle challenging neuroscience questions.

CLEM Workflows:

  • Preembedding ATUM/ATLAS

  • Postembedding Array Tomography

  • Freeze Fracture Immunogold Labeling

  • Ionic Liquid Cell Culture Imaging

  • Serial Block-Face SEM



Correlative light and electron microscopy: Naomi Kamasawa, Ph.D.


  • Image neurons labeled with GFP in electron microscopy using the automatic tape collecting ultramicrotome (ATUM) in combination with scanning electron microscopy (SEM).

  • Learn shuttle-and-find technique to correlate light and electron microscopy images.

  • Demonstration of high-pressure freezing / freeze-substitution and embedding.

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This course features a dedicated Correlative Light and Electron  Microscopy (CLEM) Techniques Module. If you wish to work on a CLEM project, please be sure to select the EM Course track in the application.



This course is intended for anyone interested in using imaging in their neuroscience research, including graduate students, postdoctoral or clinical researchers, and early career independent investigators.



When you click on the “APPLY” button, you will be redirected to an online application form.  Once you create an account, you will be able to save your application and return to complete it at another time. The application deadline is 5 PM EST, October 28, 2019.

Please be aware that the form will request the following (be sure to upload all documents in pdf format):

  • CV

  • Research Statement: In approximately 500 words, please tell us why you are interested in this course, and how this course will contribute to your ongoing or future research.

  • Reference Letter: Contact information for 2 references (name, institutional affiliation, and email address).


For CLEM EM Module applicants, please include answers to the following questions:

  • Why are you interested in learning CLEM?

  • What kind of specimens (e.g. brain tissue, slice culture, cells, etc.) do you want to work on?

  • List previous EM experience

APPLICATION DEADLINE: 5 PM EST Monday, October 28, 2019
NOTE: All application materials must be submitted no later than the application deadline. Decisions will be made approximately two weeks following the application deadline.  Please email if you have any questions about the application.

Application Period Closed

Registration Information

If you are chosen to participate in the course, you will receive an email that contains detailed registration and payment instructions. At this time, information will also be available to assist you in making travel plans.


Registration fees include all aspects of course participation and all meals. Those who register for a “shared room” will be housed in a double-occupancy hotel room and be provided transportation to and from the course location. Those who register for a “single room” will be housed in a single-occupancy hotel room and be provided transportation to and from the course location.

  • Registration only: $2,000
  • Registration Fee + Shared Room: $3,099
  • Registration Fee + Single Room: $4,197


Travel Grant Information

A limited number of travel grants are available to support lodging and travel costs for selected participants to attend the 2020 Neuroimaging Techniques Course at MPFI. Applicants will be asked to provide a justification for requesting support to be considered for a travel grant. Requests for travel grants will not affect selection decisions made by the selection committee.

Travel grants to attend the 2020 Neuroimaging Techniques Course at MPFI are generously sponsored by the Max Planck Florida Scientific Fellows Program.


Those who register for a shared or single room will be housed at Marriott Courtyard Jupiter hotel. The check-in date for all rooms is February 3; check-out is February 16. You can indicate on your registration form whether you will need to stay extra nights prior to the start of the meeting and/or after the meeting (early arrival and late departure fees will be charged). During the course, a shuttle is arranged for course participants to travel to and from the institute.



Breakfast, lunch and dinner will be offered to all course participants in the Dreyfoos Atrium with the exception of outdoor activity day (dinner on your own). If you have any special dietary requests, please contact the events coordinator.



Three airports are located near our institute:

  • Palm Beach International Airport (PBI) 16 miles

  • Fort Lauderdale International Airport (FLL) 63 miles

  • Miami International Airport (MIA) 85 miles

Past Event Photos


Miriam Chun
Events Coordinator


For more information regarding sponsorship opportunities, please contact