ICBC Led by

Timothy Ebner, Medical School and Suhasa Kodandaramaiah, Medical School & College for Science and Engineering.

The Imaging Cells during Behavior Core develops and offer a range of cutting-edge imaging tools that permit researchers to monitor brain activity.

P30DA048742-01A1, sub-project 6727

Mission/Background

The Imaging Cells during Behavior Core (ICBC) aims to provide imaging tools, computational software, and engineering expertise to neuroscience researchers investigating the brain during behavior. In addition to providing services with established tools, the ICBC also innovates new technologies to improve neural imaging capabilities.

CURRENT SERVICES

Experimental development and design

The ICBC will provide consultation to clients to help formulate a strategy for the best imaging and behavioral technique to utilize. This will include meeting with the ICBC manager to discuss experimental needs and timelines.

Design and fabrication of transparent polymer skulls

The ICBC can customize transparent polymer skulls (See-Shells) for new applications and various brain regions of interest. We can also provide full assembly of the transparent polymer skulls so they are ready for surgical implantation.

Surgical implantation of imaging devices

The ICBC can provide direct help and training with surgical implantation of the custom brain windows based on specific experimental needs of the client. Proper use of anesthesia, animal monitoring (perioperative and postoperative), and aseptic surgical techniques will all be covered.

Development and assembly of miniaturized imaging devices

We can fabricate and set up miniscopes and mini-mscopes which are used to investigate neural circuits in freely behaving mice. Additionally, we provide engineering consultation to modify current device designs to target other brain regions of interest. We are currently implementing a miniscope to image in the nucleus accumbens. We are using mini-mscopes to image cortex-wide neural activity in mice during a variety of sensory evoked stimuli and during social behavior.

a) Computer-aided design (CAD) model of the mini-mscope used for calcium imaging across the dorsal cortex. b) Computer-numerically controlled (CNC) machined mini-mscope fabricated from the CAD model in (a). c) Left: image of a mouse bearing the mini-mscope and engaging in natural behaviors such as rearing. Right: image of the dorsal cortex captured with the mini-mscope during free behavior.

Wide-field calcium imaging

The ICBC has the capability to perform wide-field calcium imaging in awake head-fixed mice. The equipment available includes use of dual-wavelength hemodynamic correction for GCaMP, and the ability for simultaneous calcium imaging with optogenetics. Development and refinement of experimental design as well as training in use of the imaging equipment will be provided by the ICBC.

Two-photon (2P) imaging assistance

The ICBC will work with the University Imaging Center (UIC) to help provide training and setup for performing 2P imaging (structural or functional) in anesthetized or awake head-fixed animals. Additional training and assistance can also be provided for analyzing 2P data using available software packages, such as FiJi, Suite2p, and developing custom MATLAB scripts.

Fiber photometry

The ICBC will soon provide access to fiber photometry of subcortical brain structures in freely moving or head-fixed mice. Genetically encoded sensors for calcium, dopamine, and other signals will be available. Assistance will be provided with intracranial virus injections, headpost and optical fiber implantation, behavioral task design, and image acquisition and analysis.

AI-based behavioral video monitoring and analysis in rodents

The ICBC will work with users to integrate high-speed video monitoring to their existing experiments, or provide existing equipment for head-fixed behavioral experimentation including treadmills and BPOD finite-state-machines to coordinate cue and reward deliveries. Pipelines including state of the art AI-based behavioral tracking and unsupervised behavioral segmentation (i.e. DeepLabCut, and B-SOID) can extract more detailed representations of behaviors in a fraction of the time that hand-labeling would take. Code and training will be provided to users as well as assistance in developing customized code.

Data preprocessing and analysis

The ICBC has several analytical pipelines available for clients to use on the imaging data and will provide assistance and training in implementing them. These include preprocessing steps, such as data compression, to hemodynamic correction of calcium imaging data, image stabilization, and co-registration. Further data analytical tools include algorithms for functional segmentation and functional connectivity. The ICBC can also help develop new analytical tools for specific data analyses.

IACUC protocol amendments

The ICBC will provide assistance with developing IACUC protocol amendments based on the surgical and behavioral procedures used in the ICBC and of the specific experimental need.

About

The ICBC was established as part of the Center for Neural Circuits in Addiction at the University of Minnesota in November 2019. The core is co-led by Dr. Timothy Ebner and Dr. Suhasa Kodandaramaiah and managed by Dr. Russell Carter. We have two locations on the University’s Twin Cities Campus: Lions Research Building (Room 470) and Mechanical Engineering (Room 331).

ICBC Staff

Timothy Ebner, MD, PhD. Dr. Timothy Ebner is a professor and Head of the Department of Neuroscience. His laboratory is interested in how information in the brain is represented spatially and temporally in populations of neurons during behavior. Dr. Ebner co-leads the ICBC with Dr. Kodandaramaiah.

Suhasa Kodandaramaiah, PhD. Dr. Suhasa Kodandaramaiah is an Assistant Professor in the Department of Mechanical Engineering at the University of Minnesota. His laboratory focuses on engineering neurotechnologies to interface with the brain at multiple spatial and temporal scales. These include robotic tools for single cell recording/manipulation and 3D printed polymer implants for large scale neural activity readout and perturbation. Dr. Kodandaramaiah co-leads the ICBC with Dr. Ebner.

Manny Esguerra, PhD. Dr. Manuel Esguerra (Researcher 6) has conducted neuroscience research at the University of Minnesota for over 20 years. He has extensive experience with in vivo and in vitro methods for electrophysiology and calcium imaging.

Russell Carter, PhD. Dr. Russell Carter (Researcher 6) serves as the Manager of the ICBC, and has been working in Dr. Ebner’s lab since 2013. He has extensive knowledge on mouse surgical techniques as well as calcium imaging – both mesoscale and two-photon – and behavioral imaging in mice.

Justin Aronson. Justin is a member of the Ebner lab where his daily work revolves around designing/building behavioral experiments and wide-field calcium imaging setups as well as developing data analysis pipelines. His background is in Neuroscience and Computer Science. Justin serves as the main point of contact for projects requiring behavioral monitoring and analysis. He also provides training and assistance with the implementation of analysis packages and equipment setup.

Daniel Surinach. Daniel received his B.S. in Engineering Science and Mechanics with a concentration in Biomechanics, Mechanobiology, and Math from Virginia Tech in 2018. Following his undergraduate studies, he completed his M.Sc. in Mechanical Engineering with a concentration in Mechatronics from the University of Minnesota in 2020. He is a research engineer who splits time between the ICBC and the Biosensing and Biorobotics Laboratory. Daniel works on developing novel technologies and computational strategies for whole-cortex neural sensing in freely behaving mice.

Vijay Rajendran. Vijay received his M.S. in Biomedical Engineering at the University of Minnesota in 2019 and his B.S. in Materials Science from the University of Illinois at Urbana-Champaign in 2015. He is a research engineer who splits time between the ICBC and the Biosensing and Biorobotics Laboratory. Vijay works on customizing and building miniaturized imaging devices for addiction researchers. He is also working on expanding applications of transparent polymer skulls (See-Shells) in addiction research.

Publications

Ghanbari, L., Carter, R.E., Rynes, M.L. et al. Cortex-wide neural interfacing via transparent polymer skulls. Nat Commun 10, 1500 (2019). https://doi.org/10.1038/s41467-019-09488-0

Rynes, M.L., Surinach, D., Linn, S. et al. 2020. Miniaturized head-mounted device for whole cortex mesoscale imaging in freely behaving mice. bioRxiv. doi: https://doi.org/10.1101/2020.05.25.114892

West, S.L., Aronson, J., Popa, L.S., Carter, R.E. et al. 2020. Wide-Field Calcium Imaging of Dynamic Cortical Networks During Locomotion. bioRxiv. doi: https://doi.org/10.1101/2020.07.06.189670