Report from the inaugural “4D Advanced Microscopy of Brain Circuits” course at the ZEISS Berkeley Brain Microscopy Innovation Center (BrainMIC)
The ZEISS Berkeley Brain Microscopy Innovation Center (BrainMIC) held its inaugural “4D Advanced Microscopy of Brain Circuits” course in January 2016. The intensive week-long course provided theory and hands-on experience to 16 graduate students and postdoctoral researchers eager to learn how to use the latest optical neurotechnologies of the Federal BRAIN Initiative.
“This was a really exciting course for us as we were able to build on many of our (faculty and organizers) past experiences from courses at Woods Hole and Cold Spring Harbor and add in the Berkeley technology and west coast feel to really craft something unique and relevant to the emerging neuroscience community.” Holly Aaron, Director of the BrainMIC.
Students of the 4D Advanced Microscopy course spent their mornings attending lectures on topics ranging from neural circuits, to microscopy methods for neurophysiology, to fluorophore and biosensor design. Lectures were taught by the experts, our very own UC Berkeley faculty who are leading the field in many of these areas. Student feedback on the course was overwhelmingly positive.
“Before the course I knew what buttons to click on the ZEN software to get a decent confocal image, but I didn’t understand what those buttons meant, how the microscope really worked, and how it compares to other imaging tools used in the field. Now I have a more intuitive understanding of optics and how microscopes work in general, and I am more aware of what tools are available or in development for specific imaging needs. I feel better equipped to understand and critique research involving imaging, and I know what resources to keep an eye out for as I continue my own research career here and at future institutions.”Marissa Co, PhD student at University of Texas Southwestern Medical Center.
Afternoons and evenings were spent rotating through several different imaging stations, some provided by ZEISS, others available in the BrainMIC, and still others residing in faculty laboratories. Students worked in pairs to learn a different imaging technique at each station and then developed their own personal or small group projects. Some worked with samples they brought, others in collaboration with UC Berkeley researchers, and all with the aid of organizers and company representatives, many who stayed until the late hours of the night.
“This was such a outstandingly wonderful experience for me. Rich Kramer and Marla Feller talked about courses like these being life changing and I totally agree how exposure to many of the microscopes/techniques/research can jump start a new interest/lifelong love of a topic. I am so glad to be one of the first class.” Quote from post-course student survey.
The BrainMIC course could not have been successful without the input and inspiration from our faculty, the drive and dedication of our graduate students and postdocs, the support and patience of our corporate partners, as well as the high-spirited boldness of our first class of students. For this, we extend a big thank you to everyone – lecturers and practical lab guides, ZEISS Microscopy, company representatives from ZEISS, Intelligent Imaging Innovations (3i), Bitplane, Arivis AG, and Hamamatsu, and the students who made it all worthwhile. Thank you! We are already looking forward to the next iteration.
“It was great and I loved it! I was never really too interested in microscopy as a field – generally I thought about it as just a technique, but after taking this class, I not only know so much more about the intricacies of different microscopy techniques, but I’m also very excited about those differences and how to design/choose microscopes to assay different variables.” Quote from post-course student survey.
- Holly Aaron (Director of the BrainMIC and Molecular Imaging Center)
- Jen-Yi Lee (Molecular Imaging Center)
- Georgeann Sack (Helen Wills Neuroscience Institute)
- Holly Aaron Selective plane illumination
- Keith Cheveralls Automated image analysis
- Xavier Darzacq Super resolution
- Abby Dernburg Data visualization & presentation (click to download pdf of slides)
- Dan Feldman Neural circuits; Imaging sensory maps
- Marla Feller Microscopy methods for neurophysiology
- Dan Fletcher Introduction to optics for microscopy
- Chris Gainer Imaging processing and quantification
- Hernan Garcia Basic imaging processing(click to download pdf of slides)
- Ehud Isacoff Photochemical and optogenetic tools for measuring and manipulating neural activity; Photo-activated fluorescent proteins for functional connectivity analysis
- Richard Kramer The optical revolution and neurophysiology
- Michel Maharbiz Neural Dust and other things: developing gadgets for neuroscience
- Evan Miller Fluorophore and biosensor design
- Eva Nichols Clearing agents & techniques (click to download pdf of slides)
- Nipam Patel Linear unmixing
- Laura Waller Lightfield microscopy
Practical lab guides
- Ben Shababo (Adesnik Lab)
- Rich Hakim (Adesnik Lab)
- Astou Tangara (Darzacq Lab)
- Lana Bosanac (Darzacq Lab)
- Franklin Caval-Holme (Feller Lab)
- Rémi Bos (Feller Lab)
- Niranjan Srinivas (Garcia Lab)
- Matthew Norstad (Garcia Lab)
- Augusto Quezada (Garcia Lab)
- Zach Newman (Isacoff Lab)
- Adam Hoagland (Isacoff Lab)
- Claire Oldfield (Isacoff Lab)
- Drew Friedmann (Isacoff Lab)
- Shawn Shirazi (Kaufer Lab)
- Zach Helft (Kramer Lab)
- Casey Thornton (Kramer Lab)
- Jacques Bothma (Levine/Patel Lab)
- Vadim Degtyar (Miller Lab)
- Mo Kaze (Molecular Imaging Center)
- Sam Israel (Ngai Lab)
- Paul Herzmark (retired, formerly Robey Lab)
- Eva Nichols (Saijo Lab)
- Colleen Manning (ZEISS Microscopy)
- Elise Shumsky (ZEISS Microscopy)
- Courtney Akitake (ZEISS Microscopy)
- Neeraj Gohad (ZEISS Microscopy)
- Dan Kalustian (ZEISS Microscopy)
- Alden Conner (3i)
- Lynsey Hamilton (Bitplane)
- Chris Zugates (Arivis AG)
- Michael Wussow (Arivis AG)
- John Parsons (Hamamatsu)
- Patricia Cintora (Graduate Student at University of Illinois at Urbana Champaign, Bioengineering, lab of Catherine Best Popescu)
- Marissa Co (Graduate Student at University of Texas Southwestern Medical Center, Neuroscience, lab of Genevieve Konopka)
- Ashley Frakes (Postdoc at UC Berkeley, Molecular and Cell Biology, lab of Andrew Dillin)
- Meng-meng Fu (Postdoc at Stanford University, Neurobiology, lab of Ben Barres)
- Jeongmin Kim (Graduate Student at UC Berkeley, Mechanical Engineering, lab of Xiang Zhang)
- Claire McGregor (Graduate Student at Emory University, Cell Biology, lab of Arthur English)
- Johnnie Moore-Dotson (Postdoc at University of Arizona, Physiology, lab of Erika Eggers)
- Brian Mullen (Graduate Student at UC Santa Cruz, Molecular, Cell, and Developmental Biology, lab of James Ackman)
- Helen Rankin Willsey (Postdoc at UC Berkeley, Molecular and Cell Biology, lab of Richard Harland)
- Travis Rotterman (Graduate Student at Emory University, Physiology – School of Medicine, lab of Dr. Francisco J. Alvarez)
- Kirstie Salinas (Graduate Student at UC Irvine, Neurobiology and Behavior, lab of Sunil Gandhi)
- Julie Savage (Postdoc at Laval University, Molecular Medicine, lab of Dr. Marie-Eve Tremblay)
- Konlin Shen (Graduate Student at UC Berkeley, Electical Engineering and Computer Science, lab of Michel Maharbiz)
- Peter Sohn (Graduate Student at UCSF / Gladstone Institute, Neuroscience, lab of Li Gan)
- Rebecca Voglewede (Graduate Student at Tulane University, Neuroscience, lab of Ricardo Mostany)
- Corey Webster (Graduate Student at UC Berkeley, Neurobiology division of Molecular and Cell Biology, lab of Chris Chang)
The ZEISS Berkeley BrainMIC was announced in 2014 and launched in May 2015. Today it contains some of the best commercial microscopes for fast, deep imaging and optical manipulation. Researchers are working in collaboration with ZEISS technicians to add custom hardware and develop commercially available versions of microscopes that are optimized for use with emerging neurotechnologies.
Original article by Georgeann Sack, Helen Wills Neuroscience Institute. Text & photos courtesy of the Berkeley BrainMIC, Georgeann Sack and Holly Aaron, 2016. ZEISS wishes to acknowledge the effort of the involved BrainMIC staff, organizers & speakers, our ZEISS colleagues, and the outstanding performance of the participating students and young researchers: YOU make it visible!