Thursday, November 18 | 2:00 pm

Enhancing miniscope recordings of freely behaving animals with high-resolution, multicolor Airyscan imaging

Nicolai Urban

Head of Light Microscopy
Max Planck Florida Institute for Neuroscience

Nicolai Urban is a physicist by training who has gone on to build a career in neuroscience and technology. As Head of the Light Microscopy Core at the Max Planck Florida Institute for Neuroscience (MPFI) in Jupiter, Florida, he collaborates with researchers to answer cutting edge neuroscience questions using high- and super-resolution imaging techniques, and to develop new methodologies and imaging applications. Dr. Urban specializes in STED super-resolution microscopy, a technique developed by Nobel laureate Dr. Stefan W. Hell, under whom Dr. Urban studied as a doctoral student. Dr. Urban also works as an independent consultant for Abberior Instruments America, manufacturer and distributor of STED imaging technology, and played a major role in establishing Abberior Instruments’ first North American location at the Max Planck Florida Headquarters in 2017. Prior to working with MPFI, Dr. Urban was a postdoctoral researcher at the Department of NanoBiophotonics at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, where he also earned his PhD with the rank of “summa cum laude” and defended his thesis under two Nobel laureates. He has spoken about advances in imaging at events throughout the world such as the Society for Neuroscience Conferences, SPIE Photonics West, Optics Within Life Sciences (OWLS) in Genoa, Italy, Molekulare Bildgebung (MOBI) in Göttingen, Germany, and the Joint European Magnetic Symposia in Dublin Ireland. His work has been published in many notable journals, including Nature, Neuron, and Nature Communications.


Imaging deep inside the brain while an animal is freely behaving can help us discover links between neuronal activity patterns and specific behaviors. For this, miniaturized versions of fluorescence microscopes were developed to record functional calcium dynamics without impeding an animal’s movement. Deeper brain regions are imaged by relaying the optical signal through an implanted GRIN lens, thus bypassing the otherwise prohibitive scattering inside the opaque brain tissue. Yet the cost of making these ‘miniscopes’ incredibly light in order to be head-mountable means compromising on spatial resolution, image quality, optical sectioning and multispectral imaging flexibility.
Conveniently, the implanted GRIN lens can be used to grant other microscopes access to the same field of view imaged by the miniscope. By head-fixing an animal atop a custom-built treadmill, we can visualize the previously imaged brain region with the precision of a laser scanning microscope. Using the multiplexed imaging modes of ZEISS Airyscan 2 detection we can record high-resolution multi-color volumetric data of the entire transfected brain region, as well as record visible calcium activity over extended periods of time. Taken together, this enables us to identify the visibly active neurons and distinguish which cells express one or more fluorescent labels. By co-registering these high-resolution images with the functional imaging during free behavior we can add complimentary information from secondary color channels, adding critical information about the cells that were active during behavior and creating a richer, more nuanced dataset.

In this presentation, we will explore imaging a head-fixed mouse through an implanted GRIN lens using a ZEISS LSM 980 Airyscan 2 microscope, and correlating the high-resolution multicolor images with the original behavioral dataset from the miniscope.