Applications due January 27, 2017


Course Description

The Zeiss Berkeley Brain Microscopy Innovation Center at the University of California, Berkeley offers an annual course on state-of-the-art optical tools, imaging systems, and analysis methods that are being developed for the study of neuronal circuits. Our intensive week-long course includes training in the theory and practice of emerging BRAIN Initiative neurotechnologies. Up to 16 students will work side by side with Berkeley Neuroscience faculty as they rotate through microscope demos and then choose a microscope station for a project.


We will post the 2017 agenda as it becomes available. For now, you can look at the following to get a feel for what the course is like.

>Download a pdf of last year’s agenda.

>Read about last year’s course, “New Zeiss Berkeley BrainMIC course provides training in use of state-of-the-art optical neurotechniques.”

Lecture Topics

Lectures will cover the theory and research methodology underlying the development and use of  imaging technologies for the study of neural circuits. Lectures will include the below, with more to come.

  • Neural Circuits
  • The Optical Revolution and Neurophysiology
  • Microscopy Methods for Neurophysiology
  • Clearing Agents and Techniques
  • Photochemical and optogenetic tools for measuring and manipulating neural activity
  • Fluorophore and BioSensor Design
  • Imaging Processing and Quantification
  • Imaging Sensory Maps
  • Automated Image Analysis
  • Super Resolution

Microscope stations

The course will include rotations and short research projects with your choice of over a dozen different microscope stations, as well as several offline analysis stations. Students are welcome to bring their own specimens and data to work on. Stations will include the below, with more to come.

  • Lightsheet for cleared samples
  • 2-photon in vivo imaging with 2-photon optogenetic stimulation
  • Zeiss LSM 880 NLO with FAST Airyscan
  • Spinning disk confocal with optogenetic stimulation
  • Zeiss LSM 880 NLO with NIR excitation
  • Fluorescence dissecting scope for real-time in vivo interrogation of whole embryos
  • Lightsheet for live water-based samples


The following are confirmed faculty for 2017. Check back for updates.

bateupHelen BateupAssistant Professor of NeurobiologyResearch Focus: Molecular basis of synapse and circuit changes associated with epilepsy and autism.
darzacqXavier DarzacqAssistant Professor of Genetics, Genomics and DevelopmentResearch Focus: Mechanisms of transcription regulation.
feldmanDan FeldmanProfessor of NeurobiologyResearch Focus: Sensory processing and plasticity in the somatosensory cortex.
fellerMarla FellerProfessor of NeurobiologyResearch Focus: Functional development and organization of neural circuits in the retina.
ehud_isacoff_2016_headshotEhud IsacoffProfessor of NeurobiologyResearch Focus: Mechanisms of ion channel function, synapse development, plasticity, and neural circuit function.
Na JiNa JiAssociate Professor of Physics and Molecular and Cell BiologyResearch focus: Imaging technology such as adaptive optics for the study of neural circuit activity.
kramerRichard KramerProfessor of NeurobiologyResearch Focus: Novel chemical reagents for non-invasive optical sensing and manipulation of ion channels and synapses.
millerEvan MillerAssistant Professor of Chemistry and Molecular and Cell BiologyResearch Focus: Development and application of molecular tools for studying neuroscience.
patelNipam PatelProfessor of Genetics, Genomics and DevelopmentResearch Focus: Developmental basis of evolutionary change.
wallerLaura WallerAssociate Professor of Electrical Engineering and Computer SciencesResearch Focus: designing imaging systems and algorithms.

How to Apply

PhD students, postdoctoral researchers, and early career faculty are encouraged to apply. There are three parts to the application. All application materials must be submitted by January 27th, 2017 for your application to be considered. We will notify you when your application is complete.

Part 1) Basic information. >> Please submit an application form

Part 2) Provide a statement that describes what you are studying and why you want to take the course (700 words max). Please email a pdf of your statement to brainmic@berkeley.edu. Files should be labeled with your name as follows: last_first_statement.pdf

Part 3) PhD student and postdoc applicants must submit a letter support from their PI. Please ask your PI to email a pdf of your letter of support to brainmic@berkeley.edu (700 words max). Files should be labeled using the applicant’s name as follows: last_first_support.pdf

A faculty committee will review your applications and announce our decision by February 27th.

Registration Information

If you are chosen to participate in the course, we will contact you with information on how to register, as well as information on travel and housing. A registration fee of $1200 covers the cost of the course and all meals.


The course organizers are Holly Aaron (Director of the BrainMIC and Molecular Imaging Center), Jen-Yi Lee (Molecular Imaging Center), and Georgeann Sack (Berkeley Neuroscience Communications). You can reach us by email at brainmic@berkeley.edu.

Interested in receiving updates about the course now and in future years? Join our mailing list. You can unsubscribe at any time.

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