Wide field optical imaging of brain activity

Neurovascular coupling (NVC) is the process through which changes in local neural activity are coupled to changes in cerebral blood flow.  The magnitude and location of these hemodynamic changes are tightly linked to changes in neural activity through a series of coordinated events involving neurons, glia, and vascular cells. Functional brain imaging techniques such as blood oxygen level dependent functional magnetic resonance imaging (BOLD-FMRI) rely upon hemodynamic activity, and thus NVC, to infer information about neural activity in the brain.

The most straightforward method of mapping the brain examines induced activity at a particular time after the presentation of a stimulus, for example a flickering checkerboard. This technique allows for mapping functionally specific brain activity, in this case within the visual cortex. Functionally-related brain regions also exhibit correlated neural and hemodynamic activity even in the absence of imposed tasks or overt motor movements (i.e. under “resting-state” conditions). This correlated spontaneous activity defines widely-distributed topographies known as resting state networks (RSNs) or resting-state functional connectivity (RS-FC) patterns that topographically correspond to known sensory, motor, and “cognitive” functional systems. Compared to task-based measures, RS-FC analyses have provided an efficient method for mapping the whole brain, and can be performed in patients incapable of performing tasks. Further, patterns of RS-FC are indicative of bran integrity; changes in RS-FC have been reported in a variety of neuro-psychiatric disorders including Alzheimer’s disease, depression, schizophrenia, Parkinson’s disease and stroke. Because basic functional connectional topology is conserved across mice, rats, primates, and humans, bridge measurements can be made across animal models to enrich findings in human populations.

Our lab uses light-based methods for examining brain activity in the mouse. Optical intrinsic signal imaging (OISI) takes advantage of the fact that oxygenated and deoxygenated hemoglobin differentially absorb light, so changes in light absorption can be attributed to local changes in blood volume and oxygenation. In collaboration with Joe Culver’s lab, we were the first to demonstrate RS-FC in the mouse (1), and have used OISI in a number of applications to study functional deficits and recovery in mouse models of stroke (2,3,4, 5), Alzheimer’s disease (6, 7, 8, 9, 10), and cancer (11).

Genetic engineering techniques in mice have provided new opportunities for extending wide-field optical imaging methods for assessing more directly neural activity. For example, fluctuations in calcium concentration can be imaged and visualized using fluorescent, genetically encoded calcium indicators (GECIs). These fluorophores (e.g. GCaMP) enable increased fluorescence in the presence of elevated calcium levels, and have been used extensively to study in vivo neural activity in a variety of species including C. elegans, mice, rats, and monkeys. Wide-field imaging of cortical calcium dynamics along with simultaneous imaging of hemoglobin has improved our understanding of how brain activity is altered during arousal (12) and that wide-scale organization of infra-slow activity (as reflected in RS-FC) reflects distinct brain process with its own functional and neurophysiological principles (13).

Optogenetic mapping of brain circuitry

Brain connectomics, asoriginally conceptualized, referred to axonal connectivity, i.e., white matter tracts, classically studied using histological methods. More recently, the notion of connectomics has expanded to encompass resting state functional connectivity (RS-FC) as described above. However, attempts to explain RS-FC on the basis of known anatomical connectivity have been only partially successful RS-FC can be maintained through indirect (polysynaptic) pathways. Effective connectivity (EC) is distinct from, but related to, both anatomical and functional connectivity. EC measures the influence (direct or indirect) that one brain region exerts on another. The crucial distinction between RS-FC vs. EC is that RS-FC characterizes shared spontaneous (ongoing, intrinsic) signals. By definition, pairwise RS-FC is symmetric and uninformative regarding the directionality of propagated signals. Axonal propagation in living animals is physiologically uni-directional (from cell body to axon terminal). In contrast, EC reports how activity in an identified part of the brain affects other regions. Thus, measures of EC are not necessarily symmetric, and instead capable of revealing aspects of functional connectivity obscured by network-level synchronization.

Our lab explores brain EC in the mouse using optogenetics, a technique that allows for controlling activity in genetically-defined cell populations with light. We have expanded on the OISI platform by combining it with cell-type specific optogenetic (Opto) targeting to create an Opto-OISI assay for mapping local circuitry(14). Compared to RS-FC, optogenetically-defined EC (Opto-EC) exhibits increased spatial specificity, reduced interhemispheric connectivity in regions with strong interhemispheric RS-FC, and appreciable connection strength asymmetry. Comparing the topography of Opto-EC and RS-FC patterns to maps of axonal projection connectivity from the Allen Mouse Brain Atlas, Opto-OISI mapping provides an assay that is strikingly similar to ex-vivo anterograde structural connectivity methods but in living mice (14).

We also use optogenetics to map motor movements in mice to understand how local and global brain circuitry relate to behavioral output.  Following photostimulation of the cortex, evoked motor movements in the forepaw are tracked by 2 orthogonal CMOS cameras. Using custom written motion tracking software, we can track in 3 dimension the movement amplitude and complexity of different limb movements. This method allows for quick, minimally invasive, longitudinal mapping, and can be used for monitoring recovery from brain injury as described below.

Manipulating functional recovery after stroke

All of the above techniques are employed in our lab to determine how molecular- and systems-level mechanisms of brain repair interact to influence behavioral recovery after focal ischemia in mice. Stroke causes direct structural damage to local circuits (e.g. evoked maps) and indirect functional damage to global networks (RS-FC) that can result in behavioral deficits spanning multiple domains. Neuroplasticity after stroke involves molecular changes within perilesional tissue that can be influenced by distant regions functionally connected to the site of injury. Spontaneous functional recovery can be enhanced by rehabilitative strategies, which provides experience-driven cell signaling in the brain that enhances plasticity. Optogenetics allows us to examine how increased or decreased network activity affects molecular pathways important for forming new brain circuits after stroke, as well as mapping EC of affected circuits.

Cellular contributions to neurovascular coupling

Understanding how underlying electrophysiological and/or metabolic activity relates to the local hemodynamic response is essential for interpreting blood-based mapping signals. The brain contains relatively few energy reserves and relies on its vasculature for supplying oxygen and glucose to support normal brain function. Underlying mechanisms of NVC have slowly shifted from a “feedback” model, i.e., that metabolic by-products of brain activity primarily drive CBF changes, to also include a feedforward mechanism where CBF delivery is driven by neurovascular signaling pathways. An important link connecting neural activity and CBF regulation is the ability of certain cell populations to mediate the diameter of local blood vessels through vasoactive messengers. Across several new projects, we are combining optogenetic targeting with optical intrinsic signal imaging and wide-field calcium fluorescence imaging to study how activity in different cell population contributes to local and distant changes in blood flow.


  1. White BR*, Bauer AQ*, Snyder AZ, Schlaggar BL, Lee J-M, Culver JP, “Imaging of functional connectivity in the mouse brain” PLoS One, 6(1), 2011
  2. Bauer AQ*, Kraft AW, Wright PW, Lee J-M, Culver JP, “Optical Imaging of disrupted functional connection following ischemic stroke in mice“, NeuroImage99, 2014.
  3. Hakon JC, Quattromani MJ, Sjolung C, Tomasevic G, Carey L, Lee J-M, Ruscher K, Wieloch T*, Bauer AQ*, “Multisensory stimulation improves functional recovery and resting-state functional connectivity in the mouse brain after stroke”, NeuroImage: Clinical, 17(1), 2018
  4. Kraft AW, Bauer AQ, Culver JP, Lee J-M, “Sensory Deprivation Following Focal Ischemia Accelerates Remapping and Behavioral Recovery through Arc-Dependent Synaptic Plasticity“, Science Translational Medicine, 10(426), 2018
  5. Quattromani MJ, Hakon JC, Rauch U, Bauer AQ*, Wieloch T*, “Changes in resting-state functional connectivity after stroke in a mouse brain lacking extracellular matrix components”, Neurobiology of Disease, 112(1),  2018
  6. Bero AW*, Bauer AQ*, Stewart FR, White BR, Cirrito JR, Raichle ME, Culver JP, Holtzman DM, “Bidirectional relationship between functional connectivity and A-Beta plaque deposition in mouse brain“,  Neuroscience, 32(12), 2012

    *=Co-First Authors; Featured Article

  7. Musiek ES, Lim MM, Yang G, Bauer AQ, Qi L, Roh JH, Ortiz-Gonzalez X, Culver JP, Herzog ED, Hogenesch JB, Dikranian K, Giasson BI, Weaver DR, Holtzman DM, Fitzgerald GA, “Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration”,  Clinical Investigation123(12), 2013.
  8. Liao F, Hori Y, Hudry E, Bauer AQ, Jiang H, Mahan T, Lefton K, Zhang T, Dearborn J, Kim J, Culver JP, Betensky R, Wozniak D, Hymann B, Holtzman DM, “Anti-ApoE antibody given after plaque onset decreases Aβ accumulation and improves brain function in a mouse model of Aβ amyloidosis“.  Neuroscience34(21), 2014
  9. Musiek EM, Xiong D, Patel T, Sasaki Y, Wang Y, Bauer AQ, Singh R, Finn S, Culver JP, Milbrandt J Holtzman DM, “Nmnat1 protects neuronal function without altering phospho-tau pathology in a mouse model of tauopathy“, Annals of Clinical and Translational Neurology, 3(6), 2016
  10. Griffin P, Dimitry JM, Sheehan PW, Lananna BV, Guo C, Robinette ML, Hayes ME, Cedeno MR, Hadarajah CJ, Ezerskiy LA, Colonna M, Zhang J, Bauer AQ, Burris TP, Musiek ES, “Circadian clock protein Rev-erbα regulates neuroinflammation”, PNAS, Epub ahead of print DOI:1812405116, 2019
  11. Orukari I, Siegel JS, Warrington NM, Baxter GA, Bauer AQ, Shimony JS, Rubin JB, Culver JP, “Altered hemodynamics contribute to local but not remote functional connectivity disruption due to glioma growth”,  Cerebral Blood Flow and Metabolism, In Press, Accepted July 2018
  12. Wright PW, Brier LM, Bauer AQ, Baxter GA, Kraft AW, Reisman MD, Bice AR, Snyder AZ, Lee, J-M, Culver JP, “Functional Connectivity Structure of Cortical Calcium Dynamics in Anesthetized and Awake Mice“, PLoS One, 12(10): e0185759, 2017
  13. Mitra A, Kraft AW, Wright PW, Acland B, Snyder AZ, Czerniewski L, Rosenthal Z, Bauer AQ, Snyder L, Culver JP, Lee J-M, Raichle ME, “Distinct temporal and laminar relationships in spontaneous infra-slow brain activity”, Neuron, 98(2), 2018
  14. Bauer AQ*, Kraft AW, Baxter GA, Wright PW, Reisman MD, Bice AR, Park JP, Bruchas MR, Snyder AZ, Lee, J-M, Culver JP, “Effective Connectivity Measured Using Optogenetically Evoked Hemodynamic Signals Exhibits Topography Distinct from Resting State Functional Connectivity in the Mouse“, Cerebral Cortex, 28(1), 2018