Assessing sensory versus optogenetic network activation by combining (o)fMRI with optical Ca2+ recordings

High Spatiotemporal Resolution Radial Encoding Single-Vessel fMRI

High-field preclinical functional MRI (fMRI) is enabled the high spatial resolution mapping of vessel-specific hemodynamic responses, that is single-vessel fMRI. In contrast to investigating the neuronal sources of the fMRI signal, single-vessel fMRI focuses on elucidating its vascular origin, which can be readily implemented to identify vascular changes relevant to vascular dementia or cognitive impairment. However, the limited spatial and temporal resolution of fMRI is hindered hemodynamic mapping of intracortical microvessels. Here, the radial encoding MRI scheme is implemented to measure BOLD signals of individual vessels penetrating the rat somatosensory cortex. Radial encoding MRI is employed to map cortical activation with a focal field of view (FOV), allowing vessel-specific functional mapping with 50 × 50 µm2 in-plane resolution at a 1 to 2 Hz sampling rate. Besides detecting refined hemodynamic responses of intracortical micro-venules, the radial encoding-based single-vessel fMRI enables the distinction of fMRI signals from vessel and peri-vessel voxels due to the different contribution of intravascular and extravascular effects.

Optogenetics 2.0: challenges and solutions towards a quantitative probing of neural circuits

To exploit the full potential of optogenetics, we need to titrate and tailor optogenetic methods to emulate naturalistic circuit function. For that, the following prerequisites need to be met: first, we need to target opsin expression not only to genetically defined neurons per se, but to specifically target a functional node. Second, we need to assess the scope of optogenetic modulation, i.e. the fraction of optogenetically modulated neurons. Third, we need to integrate optogenetic control in a closed loop setting. Fourth, we need to further safe and stable gene expression and light delivery to bring optogenetics to the clinics. Here, we review these concepts for the human and rodent brain.

A flexible and versatile system for multi-color fiber photometry and optogenetic manipulation

Here, we present simultaneous fiber photometry recordings and optogenetic stimulation based on a multimode fused fiber coupler for both light delivery and collection without the need for dichroic beam splitters. In combination with a multi-color light source and appropriate optical filters, our approach offers remarkable flexibility in experimental design and facilitates the exploration of new molecular tools in vivo at minimal cost. We demonstrate straightforward re-configuration of the setup to operate with green, red, and near-infrared calcium indicators with or without simultaneous optogenetic stimulation and further explore the multi-color photometry capabilities of the system. The ease of assembly, operation, characterization, and customization of this platform holds the potential to foster the development of experimental strategies for multi-color fused fiber photometry combined with optogenetics far beyond its current state.

Hemodynamic transient and functional connectivity follow structural connectivity and cell type over the brain hierarchy

The neural circuit of the brain is organized as a hierarchy of functional units with wide-ranging connections that support information flow and functional connectivity. Studies using MRI indicate a moderate coupling between structural and functional connectivity at the system level. However, how do connections of different directions (feedforward and feedback) and regions with different excitatory and inhibitory (E/I) neurons shape the hemodynamic activity and functional connectivity over the hierarchy are unknown. Here, we used functional MRI to detect optogenetic-evoked and resting-state activities over a somatosensory pathway in the mouse brain in relation to axonal projection and E/I distribution. Using a highly sensitive ultrafast imaging, we identified extensive activation in regions up to the third order of axonal projections following optogenetic excitation of the ventral posteriomedial nucleus of the thalamus. The evoked response and functional connectivity correlated with feedforward projections more than feedback projections and weakened with the hierarchy. The hemodynamic response exhibited regional and hierarchical differences, with slower and more variable responses in high-order areas and bipolar response predominantly in the contralateral cortex. Electrophysiological recordings suggest that these reflect differences in neural activity rather than neurovascular coupling. Importantly, the positive and negative parts of the hemodynamic response correlated with E/I neuronal densities, respectively. Furthermore, resting-state functional connectivity was more associated with E/I distribution, whereas stimulus-evoked effective connectivity followed structural wiring. These findings indicate that the structure-function relationship is projection-, cell-type- and hierarchy-dependent. Hemodynamic transients could reflect E/I activity and the increased complexity of hierarchical processing.

Optogenetic fMRI for Brain-Wide Circuit Analysis of Sensory Processing

Sensory processing is a complex neurological process that receives, integrates, and responds to information from one's own body and environment, which is closely related to survival as well as neurological disorders. Brain-wide networks of sensory processing are difficult to investigate due to their dynamic regulation by multiple brain circuits. Optogenetics, a neuromodulation technique that uses light-sensitive proteins, can be combined with functional magnetic resonance imaging (ofMRI) to measure whole-brain activity. Since ofMRI has increasingly been used for investigating brain circuits underlying sensory processing for over a decade, we systematically reviewed recent ofMRI studies of sensory circuits and discussed the challenges of optogenetic fMRI in rodents.

The current status and trend of the functional magnetic resonance combined with stimulation in animals

As a non-radiative, non-invasive imaging technique, functional magnetic resonance imaging (fMRI) has excellent effects on studying the activation of blood oxygen levels and functional connectivity of the brain in human and animal models. Compared with resting-state fMRI, fMRI combined with stimulation could be used to assess the activation of specific brain regions and the connectivity of specific pathways and achieve better signal capture with a clear purpose and more significant results. Various fMRI methods and specific stimulation paradigms have been proposed to investigate brain activation in a specific state, such as electrical, mechanical, visual, olfactory, and direct brain stimulation. In this review, the studies on animal brain activation using fMRI combined with different stimulation methods were retrieved. The instruments, experimental parameters, anesthesia, and animal models in different stimulation conditions were summarized. The findings would provide a reference for studies on estimating specific brain activation using fMRI combined with stimulation.

Functional States Shape the Spatiotemporal Representation of Local and Cortex-wide Neural Activity in Mouse Sensory Cortex

The spatiotemporal representation of neural activity during rest and upon sensory stimulation in cortical areas is highly dynamic, and may be predominantly governed by cortical state. On the mesoscale level, intrinsic neuronal activity ranges from a persistent state, generally associated with a sustained depolarization of neurons, to a bimodal, slow-wave like state with bursts of neuronal activation, alternating with silent periods. These different activity states are prevalent under certain types of sedatives, or are associated with specific behavioral or vigilance conditions. Neurophysiological experiments assessing circuit activity, usually assume a constant underlying state, yet reports of variability of neuronal responses under seemingly constant conditions are common in the field. Even when a certain type of neural activity or cortical state can stably be maintained over time, the associated response properties are highly relevant for explaining experimental outcomes. Here we describe the spatiotemporal characteristics of ongoing activity and sensory evoked responses under two predominant functional states in the sensory cortices of mice: persistent activity (PA) and slow wave activity (SWA). Using electrophysiological recordings, and local and wide-field calcium recordings, we examine whether spontaneous and sensory evoked neuronal activity propagate throughout the cortex in a state dependent manner. We find that PA and SWA differ in their spatiotemporal characteristics which determine the cortical network's response to a sensory stimulus. During PA state, sensory stimulation elicits gamma-based short-latency responses which precisely follow each stimulation pulse and are prone to adaptation upon higher stimulation frequencies. Sensory responses during SWA are more variable, dependent on refractory periods following spontaneous slow waves. While spontaneous slow waves propagated in anterior-posterior direction in a majority of observations, the direction of propagation of stimulus-elicited wave depends on the sensory modality. These findings suggest that cortical state explains variance and should be considered when investigating multi-scale correlates of functional neurocircuit activity.

Spectral fiber photometry derives hemoglobin concentration changes for accurate measurement of fluorescent sensor activity

Fiber photometry is an emerging technique for recording fluorescent sensor activity in the brain. However, significant hemoglobin absorption artifacts in fiber photometry data may be misinterpreted as sensor activity changes. Because hemoglobin exists widely in the brain, and its concentration varies temporally, such artifacts could impede the accuracy of photometry recordings. Here we present use of spectral photometry and computational methods to quantify photon absorption effects by using activity-independent fluorescence signals, which can be used to derive oxy- and deoxy-hemoglobin concentration changes. Although these changes are often temporally delayed compared with the fast-responding fluorescence spikes, we found that erroneous interpretation may occur when examining pharmacology-induced sustained changes and that sometimes hemoglobin absorption could flip the GCaMP signal polarity. We provide hemoglobin-based correction methods to restore fluorescence signals and compare our results with other commonly used approaches. We also demonstrated the utility of spectral fiber photometry for delineating regional differences in hemodynamic response functions.

Combining magnetic resonance imaging with readout and/or perturbation of neural activity in animal models: Advantages and pitfalls

One of the main challenges in brain research is to link all aspects of brain function: on a cellular, systemic, and functional level. Multimodal neuroimaging methodology provides a continuously evolving platform. Being able to combine calcium imaging, optogenetics, electrophysiology, chemogenetics, and functional magnetic resonance imaging (fMRI) as part of the numerous efforts on brain functional mapping, we have a unique opportunity to better understand brain function. This review will focus on the developments in application of these tools within fMRI studies and highlight the challenges and choices neurosciences face when designing multimodal experiments.

Fiber-based lactate recordings with fluorescence resonance energy transfer sensors by applying an magnetic resonance-informed correction of hemodynamic artifacts

Significance: Fluorescence resonance energy transfer (FRET) sensors offer enormous benefits when studying neurophysiology through confocal microscopy. Yet, their use for fiber-based in vivo recordings is hampered by massive confounding effects and has therefore been scarcely reported. Aim: We aim to investigate whether in vivo fiber-based lactate recordings in the rodent brain are feasible with FRET sensors and implement a correction algorithm for the predominant hemodynamic artifact. Approach: We performed fiber-based FRET recordings of lactate (Laconic) and calcium (Twitch-2B) simultaneously with functional MRI and pharmacological MRI. MR-derived parameters were applied to correct hemodynamic artifacts. Results of FRET measurements were validated by local field potential, magnetic resonance spectroscopy, and blood analysis. Results: Hemodynamic artifacts dominated fiber-based in vivo FRET measurements with both Laconic and Twitch-2B. Our MR-based correction algorithm enabled to remove the artifacts and detect lactate and calcium changes during sensory stimulation or intravenous lactate injections. Conclusions: In vivo fiber-based lactate recordings are feasible using FRET-based sensors. However, signal corrections are required. MR-derived hemodynamic parameters can successfully be applied for artifact correction.

Connecting the dots between cell populations, whole-brain activity, and behavior

Simultaneously manipulating and monitoring both microscopic and macroscopic brain activity in vivo and identifying the linkage to behavior are powerful tools in neuroscience research. These capabilities have been realized with the recent technical advances of optogenetics and its combination with fMRI, here termed "opto-fMRI." Opto-fMRI allows for targeted brain region-, cell-type-, or projection-specific manipulation and targeted Ca 2 + activity measurement to be linked with global brain signaling and behavior. We cover the history, technical advances, applications, and important considerations of opto-fMRI in anesthetized and awake rodents and the future directions of the combined techniques in neuroscience and neuroimaging.

Building bridges: simultaneous multimodal neuroimaging approaches for exploring the organization of brain networks

Brain organization is evident across spatiotemporal scales as well as from structural and functional data. Yet, translating from micro- to macroscale (vice versa) as well as between different measures is difficult. Reconciling disparate observations from different modes is challenging because each specializes within a restricted spatiotemporal milieu, usually has bounded organ coverage, and has access to different contrasts. True intersubject biological heterogeneity, variation in experiment implementation (e.g., use of anesthesia), and true moment-to-moment variations in brain activity (maybe attributable to different brain states) also contribute to variability between studies. Ultimately, for a deeper and more actionable understanding of brain organization, an ability to translate across scales, measures, and species is needed. Simultaneous multimodal methods can contribute to bettering this understanding. We consider four modes, three optically based: multiphoton imaging, single-photon (wide-field) imaging, and fiber photometry, as well as magnetic resonance imaging. We discuss each mode as well as their pairwise combinations with regard to the definition and study of brain networks.

Beyond correlation: functional OPTO-MAgnetic Integration Concept (OPTOMAIC) to reveal the brain-wide signature of local neuronal signals-of-interest

Significance: Due to the vascular origin of the fMRI signal, the spatiotemporally precise interpretation of the blood oxygen level-dependent (BOLD) response as brain-wide correlate of neuronal activity is limited. Optical fiber-based neuronal calcium recordings provide a specific and temporally highly resolved signal yet lacking brain-wide coverage. The cross-modal integration of both modalities holds the potential for unique synergies. Aim: The OPTO-MAgnetic Integration Concept (OPTOMAIC) extracts the very fraction of the BOLD response that reacts to optically recorded neuronal signals-of-interest. Approach and Results: First, OPTOMAIC identifies the trials containing neuronal signal-of-interest (SoI) in the optical recordings. The long duration of the BOLD response is considered by calculating and thresholding neuronal interevent intervals. The resulting optical regression vector is probed for a positive BOLD response with single-event and single-voxel resolution, generating a BOLD response matrix containing only those events and voxels with both a neuronal SoI and a positive fMRI signal increase. Last, the onset of the BOLD response is being quantified, representing the section of the BOLD response most reliably reporting at least components of the neuronal signal. Conclusions: The seven OPTOMAIC steps result in a brain-wide BOLD signature reflecting the underlying neuronal SoI with utmost cross-modal integration depth and taking full advantage of the specific strengths of each method.

Computing hemodynamic response functions from concurrent spectral fiber-photometry and fMRI data

Significance: Although emerging evidence suggests that the hemodynamic response function (HRF) can vary by brain region and species, a single, canonical, human-based HRF is widely used in animal studies. Therefore, the development of flexible, accessible, brain-region specific HRF calculation approaches is paramount as hemodynamic animal studies become increasingly popular. Aim: To establish an fMRI-compatible, spectral, fiber-photometry platform for HRF calculation and validation in any rat brain region. Approach: We used our platform to simultaneously measure (a) neuronal activity via genetically encoded calcium indicators (GCaMP6f), (b) local cerebral blood volume (CBV) from intravenous Rhodamine B dye, and (c) whole brain CBV via fMRI with the Feraheme contrast agent. Empirical HRFs were calculated with GCaMP6f and Rhodamine B recordings from rat brain regions during resting-state and task-based paradigms. Results: We calculated empirical HRFs for the rat primary somatosensory, anterior cingulate, prelimbic, retrosplenial, and anterior insular cortical areas. Each HRF was faster and narrower than the canonical HRF and no significant difference was observed between these cortical regions. When used in general linear model analyses of corresponding fMRI data, the empirical HRFs showed better detection performance than the canonical HRF. Conclusions: Our findings demonstrate the viability and utility of fiber-photometry-based HRF calculations. This platform is readily scalable to multiple simultaneous recording sites, and adaptable to study transfer functions between stimulation events, neuronal activity, neurotransmitter release, and hemodynamic responses.

Combined resting state-fMRI and calcium recordings show stable brain states for task-induced fMRI in mice under combined ISO/MED anesthesia

For fMRI in animal models, the combination of low-dose anesthetic, isoflurane (ISO), and the sedative medetomidine (MED) has recently become an advocated regimen to achieve stable neuronal states and brain networks in rats that are required for reliable task-induced BOLD fMRI. However, in mice the temporal stability of neuronal states and networks in resting-state (rs)-fMRI experiments during the combined ISO/MED regimen has not been systematically investigated. Using a multimodal approach with optical calcium (Ca²⁺) recordings and rs-fMRI, we investigated cortical neuronal/astrocytic Ca²⁺activity states and brain networks at multiple time points while switching from anesthesia with 1% ISO to a combined ISO/MED regimen. We found that cortical activity states reached a steady-state 45 min following start of MED infusion as indicated by stable Ca²⁺ transients. Similarly, rs-networks were not statistically different between anesthesia with ISO and the combined ISO/MED regimen 45 and 100 min after start of MED. Importantly, during the transition time we identified changed rs-network signatures that likely reflect the different mode of action of the respective anesthetic; these included a dose-dependent increase in cortico-cortical functional connectivity (FC) presumably caused by reduction of ISO concentration and decreased FC in subcortical arousal nuclei due to MED infusion. Furthermore, we report detection of visual stimulation-induced BOLD fMRI during the stable ISO/MED neuronal state 45 min after induction. Based on our findings, we recommend a 45-minute waiting period after switching from ISO anesthesia to the combined ISO/MED regimen before performing rs- or task-induced fMRI experiments.

One-pot synthesis of carboxymethyl-dextran coated iron oxide nanoparticles (CION) for preclinical fMRI and MRA applications

Superparamagnetic iron-oxide nanoparticles are robust contrast agents for magnetic resonance imaging (MRI) used for sensitive structural and functional mapping of the cerebral blood volume (CBV) when administered intravenously. To date, many CBV-MRI studies are conducted with Feraheme, manufactured for the clinical treatment of iron-deficiency. Unfortunately, Feraheme is currently not available outside the United States due to commercial and regulatory constraints, making CBV-MRI methods either inaccessible or very costly to achieve. To address this barrier, we developed a simple, one-pot recipe to synthesize Carboxymethyl-dextran coated Iron Oxide Nanoparticles, namely, “CION”, suitable for preclinical CBV-MRI applications. Here we disseminate a step-by-step instruction of our one-pot synthesis protocol, which allows CION to be produced in laboratories with minimal cost. We also characterized different CION-conjugations by manipulating polymer to metal stoichiometric ratio in terms of their size, surface chemistry, and chemical composition, and shifts in MR relaxivity and pharmacokinetics. We performed several proof-of-concept experiments in vivo, demonstrating the utility of CION for functional and structural MRI applications, including hypercapnic CO₂ challenge, visual stimulation, targeted optogenetic stimulation, and microangiography. We also present evidence that CION can serve as a cross-modality research platform by showing concurrent in vivo optical and MRI measurement of CBV using fluorescent-labeled CION. The simplicity and cost-effectiveness of our one-pot synthesis method should allow researchers to reproduce CION and tailor the relaxivity and pharmacokinetics according to their imaging needs. It is our hope that this work makes CBV-MRI more openly available and affordable for a variety of research applications.

Contribution of Excitatory and Inhibitory Neuronal Activity to BOLD fMRI

The BOLD fMRI response in the cortex is often assumed to reflect changes in excitatory neural activity. However, the contribution of inhibitory neurons to BOLD fMRI is unclear. Here, the role of inhibitory and excitatory activity was examined using multimodal approaches: electrophysiological recording, 15.2 T fMRI, optical intrinsic signal imaging, and modeling. Inhibitory and excitatory neuronal activity in the somatosensory cortex were selectively modulated by 20-s optogenetic stimulation of VGAT-ChR2 and CaMKII-ChR2 mice, respectively. Somatosensory stimulation and optogenetic stimulation of excitatory neurons induced positive BOLD responses in the somatosensory network, whereas stimulation of inhibitory neurons produced biphasic responses at the stimulation site, initial positive and later negative BOLD signals, and negative BOLD responses at downstream sites. When the stimulation duration was reduced to 5 s, the hemodynamic response of VGAT-ChR2 mice to optogenetic stimulation was only positive. Lastly, modeling performed from neuronal and hemodynamic data shows that the hemodynamic response function (HRF) of excitatory neurons is similar across different conditions, whereas the HRF of inhibitory neurons is highly sensitive to stimulation frequency and peaks earlier than that of excitatory neurons. Our study provides insights into the neurovascular coupling of excitatory and inhibitory neurons and the interpretation of BOLD fMRI signals.

Retrosplenial Cortex Contributes to Network Changes during Seizures in the GAERS Absence Epilepsy Rat Model

Resting state-fMRI was performed to explore brain networks in Genetic Absence Epilepsy Rats from Strasbourg and in nonepileptic controls (NEC) during monitoring of the brain state by simultaneous optical Ca2+-recordings. Graph theoretical analysis allowed for the identification of acute and chronic network changes and revealed preserved small world topology before and after seizure onset. The most prominent acute change in network organization during seizures was the segregation of cortical regions from the remaining brain. Stronger connections between thalamic with limbic regions compared with preseizure state indicated network regularization during seizures. When comparing between strains, intrathalamic connections were prominent in NEC, on local level represented by higher thalamic strengths and hub scores. Subtle differences were observed for retrosplenial cortex (RS), forming more connections beyond cortex in epileptic rats, and showing a tendency to lateralization during seizures. A potential role of RS as hub between subcortical and cortical regions in epilepsy was supported by increased numbers of parvalbumin-positive (PV+) interneurons together with enhanced inhibitory synaptic activity and neuronal excitability in pyramidal neurons. By combining multimodal fMRI data, graph theoretical methods, and electrophysiological recordings, we identified the RS as promising target for modulation of seizure activity and/or comorbidities.

Exploring two-photon optogenetics beyond 1100 nm for specific and effective all-optical physiology

Two-photon (2-P) all-optical approaches combine in vivo 2-P calcium imaging and 2-P optogenetic modulations. Here, firstly, we combined in vivo juxtacellular recordings and GCaMP6f-based 2-P calcium imaging in mouse visual cortex to tune our detection algorithm towards a 100% specific identification of action potential-related calcium transients. Secondly, we minimized photostimulation artifacts by using extended-wavelength-spectrum laser sources for optogenetic stimulation. We achieved artifact-free all-optical experiments performing optogenetic stimulation from 1100 nm to 1300 nm. Thirdly, we determined the spectral range for maximizing efficacy until 1300 nm. The rate of evoked transients in GCaMP6f/C1V1-co-expressing cortical neurons peaked already at 1100 nm. By refining spike detection and defining 1100 nm as the optimal wavelength for artifact-free and effective GCaMP6f/C1V1-based all-optical physiology, we increased the translational value of these approaches, e.g., for the development of network-based therapies.

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We developed an algorithm for 100 %-specific identification of AP-related calcium transients

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Artifact-free all-optical experiments can be achieved from 1100 nm to 1300 nm

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Efficacy of C1V1 excitation does not increase beyond 1100 nm until 1300 nm

Multimode Optical Fibers for Optical Neural Interfaces

Although multiphoton microscopy enables optical control and monitoring of neural activity with single cells resolution over a depth of several hundreds of micrometers, the scattering nature of the brain tissue requires implantable optical neural interfaces to access subcortical structures. If micro light-emitting devices (μLEDs) and solid-state waveguides represent important technological advancements for the field, multimodal optical fibers (MMFs) are still the most diffused tool in neuroscience labs to interface with deep regions of the brain. At a first glance, MMFs can be seen as very limited systems. However, new studies and discoveries in optics, photonics, and technological solutions for their application to neuroscience research have enabled applications of MMF where competing technologies fail. In this framework, the chapter starts with a description of optical neural interfaces based on MMF, with specific reference on recent works analyzing the performances of this approach to deliver and collect light from scattering tissue. The discussion then focuses on how peculiar features of MMFs can be exploited to obtain unconventional applications, including brain imaging through a single multimode fiber, multifunctional neural interfaces, and depth-resolved light delivery and functional fluorescence collection.

A selected review of recent advances in the study of neuronal circuits using fiber photometry

To understand the correlation between animal behaviors and the underlying neuronal circuits, it is important to monitor and record neurotransmission in the brain of freely moving animals. With the development of fiber photometry, based on genetically encoded biosensors, and novel electrochemical biosensors, it is possible to measure some key neuronal transmission events specific to cell types or neurotransmitters of interest with high temporospatial resolution. This review discusses the recent advances and achievements of these two techniques in the study of neurotransmission in animal models and how they can be used to complement other techniques in the neuroscientist's toolbox.

Ray tracing models for estimating light collection properties of microstructured tapered optical fibers for optical neural interfaces

Tapered optical fibers (TFs) were recently employed for depth-resolved monitoring of functional fluorescence in subcortical brain structures, enabling light collection from groups of a few cells through small optical windows located on the taper edge [Pisano et al., Nat. Methods16, 1185 (2019)1548-709110.1038/s41592-019-0581-x]. Here we present a numerical model to estimate light collection properties of microstructured TFs implanted in scattering brain tissue. Ray tracing coupled with the Henyey-Greenstein scattering model enables the estimation of both light collection and fluorescence excitation fields in three dimensions, whose combination is employed to retrieve the volume of tissue probed by the device.

Brain states govern the spatio-temporal dynamics of resting-state functional connectivity

Previously, using simultaneous resting-state functional magnetic resonance imaging (fMRI) and photometry-based neuronal calcium recordings in the anesthetized rat, we identified blood oxygenation level-dependent (BOLD) responses directly related to slow calcium waves, revealing a cortex-wide and spatially organized correlate of locally recorded neuronal activity (Schwalm et al., 2017). Here, using the same techniques, we investigate two distinct cortical activity states: persistent activity, in which compartmentalized network dynamics were observed; and slow wave activity, dominated by a cortex-wide BOLD component, suggesting a strong functional coupling of inter-cortical activity. During slow wave activity, we find a correlation between the occurring slow wave events and the strength of functional connectivity between different cortical areas. These findings suggest that down-up transitions of neuronal excitability can drive cortex-wide functional connectivity. This study provides further evidence that changes in functional connectivity are dependent on the brain's current state, directly linked to the generation of slow waves.

Mapping the Brain-Wide Network Effects by Optogenetic Activation of the Corpus Callosum

Optogenetically driven manipulation of circuit-specific activity enables causality studies, but its global brain-wide effect is rarely reported. Here, we applied simultaneous functional magnetic resonance imaging (fMRI) and calcium recording with optogenetic activation of the corpus callosum (CC) connecting barrel cortices (BC). Robust positive BOLD was detected in the ipsilateral BC due to antidromic activity, spreading to the ipsilateral motor cortex (MC), and posterior thalamus (PO). In the orthodromic target, positive BOLD was reliably evoked by 2 Hz light pulses, whereas 40 Hz light pulses led to reduced calcium, indicative of CC-mediated inhibition. This presumed optogenetic CC-mediated inhibition was further elucidated by pairing light pulses with whisker stimulation at varied interstimulus intervals. Whisker-induced positive BOLD and calcium signals were reduced at intervals of 50/100 ms. The calcium-amplitude-modulation-based correlation with whole-brain fMRI signal revealed that the inhibitory effects spread to contralateral BC, ipsilateral MC, and PO. This work raises the need for fMRI to elucidate the brain-wide network activation in response to optogenetic stimulation.

The (Un)Conscious Mouse as a Model for Human Brain Functions: Key Principles of Anesthesia and Their Impact on Translational Neuroimaging

In recent years, technical and procedural advances have brought functional magnetic resonance imaging (fMRI) to the field of murine neuroscience. Due to its unique capacity to measure functional activity non-invasively, across the entire brain, fMRI allows for the direct comparison of large-scale murine and human brain functions. This opens an avenue for bidirectional translational strategies to address fundamental questions ranging from neurological disorders to the nature of consciousness. The key challenges of murine fMRI are: (1) to generate and maintain functional brain states that approximate those of calm and relaxed human volunteers, while (2) preserving neurovascular coupling and physiological baseline conditions. Low-dose anesthetic protocols are commonly applied in murine functional brain studies to prevent stress and facilitate a calm and relaxed condition among animals. Yet, current mono-anesthesia has been shown to impair neural transmission and hemodynamic integrity. By linking the current state of murine electrophysiology, Ca2+ imaging and fMRI of anesthetic effects to findings from human studies, this systematic review proposes general principles to design, apply and monitor anesthetic protocols in a more sophisticated way. The further development of balanced multimodal anesthesia, combining two or more drugs with complementary modes of action helps to shape and maintain specific brain states and relevant aspects of murine physiology. Functional connectivity and its dynamic repertoire as assessed by fMRI can be used to make inferences about cortical states and provide additional information about whole-brain functional dynamics. Based on this, a simple and comprehensive functional neurosignature pattern can be determined for use in defining brain states and anesthetic depth in rest and in response to stimuli. Such a signature can be evaluated and shared between labs to indicate the brain state of a mouse during experiments, an important step toward translating findings across species.

Oscillations in the auditory system and their possible role

GOURÉVITCH, B., C. Martin, O. Postal, J.J. Eggermont. Oscillations in the auditory system, their possible role. NEUROSCI BIOBEHAV REV XXX XXX-XXX, 2020. - Neural oscillations are thought to have various roles in brain processing such as, attention modulation, neuronal communication, motor coordination, memory consolidation, decision-making, or feature binding. The role of oscillations in the auditory system is less clear, especially due to the large discrepancy between human and animal studies. Here we describe many methodological issues that confound the results of oscillation studies in the auditory field. Moreover, we discuss the relationship between neural entrainment and oscillations that remains unclear. Finally, we aim to identify which kind of oscillations could be specific or salient to the auditory areas and their processing. We suggest that the role of oscillations might dramatically differ between the primary auditory cortex and the more associative auditory areas. Despite the moderate presence of intrinsic low frequency oscillations in the primary auditory cortex, rhythmic components in the input seem crucial for auditory processing. This allows the phase entrainment between the oscillatory phase and rhythmic input, which is an integral part of stimulus selection within the auditory system.

Animal Functional Magnetic Resonance Imaging: Trends and Path Toward Standardization

Animal whole-brain functional magnetic resonance imaging (fMRI) provides a non-invasive window into brain activity. A collection of associated methods aims to replicate observations made in humans and to identify the mechanisms underlying the distributed neuronal activity in the healthy and disordered brain. Animal fMRI studies have developed rapidly over the past years, fueled by the development of resting-state fMRI connectivity and genetically encoded neuromodulatory tools. Yet, comparisons between sites remain hampered by lack of standardization. Recently, we highlighted that mouse resting-state functional connectivity converges across centers, although large discrepancies in sensitivity and specificity remained. Here, we explore past and present trends within the animal fMRI community and highlight critical aspects in study design, data acquisition, and post-processing operations, that may affect the results and influence the comparability between studies. We also suggest practices aimed to promote the adoption of standards within the community and improve between-lab reproducibility. The implementation of standardized animal neuroimaging protocols will facilitate animal population imaging efforts as well as meta-analysis and replication studies, the gold standards in evidence-based science.

A cortical rat hemodynamic response function for improved detection of BOLD activation under common experimental conditions

For a reliable estimation of neuronal activation based on BOLD fMRI measurements an accurate model of the hemodynamic response is essential. Since a large part of basic neuroscience research is based on small animal data, it is necessary to characterize a hemodynamic response function (HRF) which is optimized for small animals. Therefore, we have determined and investigated the HRFs of rats obtained under a variety of experimental conditions in the primary somatosensory cortex. Measurements were performed on animals of different sex and strain, under different anesthetics, with and without ventilation and using different stimulation modalities. All modalities of stimulation used in this study induced neuronal activity in the primary somatosensory cortex or in subcortical regions. Since the HRFs of the BOLD responses in the primary somatosensory cortex showed a close concordance for the different conditions, we were able to determine a cortical rat HRF. This HRF is based on 143 BOLD measurements of 76 rats and can be used for statistical parametric mapping. It showed substantially faster progression than the human HRF, with a maximum after 2.8 ± 0.8 s, and a following undershoot after 6.1 ± 3.7 s. If the rat HRF was used statistical analysis of rat data showed a significantly improved detection performance in the somatosensory cortex in comparison to the commonly used HRF based on measurements in humans.

Mapping optogenetically-driven single-vessel fMRI with concurrent neuronal calcium recordings in the rat hippocampus

Extensive in vivo imaging studies investigate the hippocampal neural network function, mainly focusing on the dorsal CA1 region given its optical accessibility. Multi-modality fMRI with simultaneous hippocampal electrophysiological recording reveal broad cortical correlation patterns, but the detailed spatial hippocampal functional map remains lacking given the limited fMRI resolution. In particular, hemodynamic responses linked to specific neural activity are unclear at the single-vessel level across hippocampal vasculature, which hinders the deciphering of the hippocampal malfunction in animal models and the translation to critical neurovascular coupling (NVC) patterns for human fMRI. We simultaneously acquired optogenetically-driven neuronal Ca2+ signals with single-vessel blood-oxygen-level-dependent (BOLD) and cerebral-blood-volume (CBV)-fMRI from individual venules and arterioles. Distinct spatiotemporal patterns of hippocampal hemodynamic responses were correlated to optogenetically evoked and spreading depression-like calcium events. The calcium event-related single-vessel hemodynamic modeling revealed significantly reduced NVC efficiency upon spreading depression-like (SDL) events, providing a direct measure of the NVC function at various hippocampal states.

Functional MRI Readouts From BOLD and Diffusion Measurements Differentially Respond to Optogenetic Activation and Tissue Heating

Functional blood-oxygenation-level-dependent (BOLD) MRI provides a brain-wide readout that depends on the hemodynamic response to neuronal activity. Diffusion fMRI has been proposed as an alternative to BOLD fMRI and has been postulated to directly rely on neuronal activity. These complementary functional readouts are versatile tools to be combined with optogenetic stimulation to investigate networks of the brain. The cell-specificity and temporal precision of optogenetic manipulations promise to enable further investigation of the origin of fMRI signals. The signal characteristics of the diffusion fMRI readout vice versa may better resolve network effects of optogenetic stimulation. However, the light application needed for optogenetic stimulation is accompanied by heat deposition within the tissue. As both diffusion and BOLD are sensitive to temperature changes, light application can lead to apparent activations confounding the interpretation of fMRI data. The degree of tissue heating, the appearance of apparent activation in different fMRI sequences and the origin of these phenomena are not well understood. Here, we disentangled apparent activations in BOLD and diffusion measurements in rats from physiological activation upon sensory or optogenetic stimulation. Both, BOLD and diffusion fMRI revealed similar signal shapes upon sensory stimulation that differed clearly from those upon heating. Apparent activations induced by high-intensity light application were dominated by T₂^∗-effects and resulted in mainly negative signal changes. We estimated that even low-intensity light application used for optogenetic stimulation reduces the BOLD response close to the fiber by up to 0.4%. The diffusion fMRI signal contained T₂, T₂^∗ and diffusion components. The apparent diffusion coefficient, which reflects the isolated diffusion component, showed negative changes upon both optogenetic and electric forepaw stimulation. In contrast, positive changes were detected upon high-intensity light application and thus ruled out heating as a major contributor to the diffusion fMRI signal.

Depth-resolved fiber photometry with a single tapered optical fiber implant

Fiber photometry is increasingly utilized to monitor fluorescent sensors of neural activity in the brain. However, most implementations are based on flat-cleaved optical fibers that can only interface with shallow tissue volumes adjacent to the fiber. We exploit modal properties of tapered optical fibers (TFs) to enable light collection over an extent of up to 2 mm of tissue and multisite photometry along the taper. Using a single TF, we simultaneously observed distinct dopamine transients in dorsal and ventral striatum in freely moving mice performing a simple, operant conditioning task. Collection volumes from TFs can also be engineered in both shape and size by microstructuring the nonplanar surface of the taper, to optically target multiple sites not only in the deep brain but, in general, in any biological system or organ in which light collection is beneficial but challenging because of light scattering and absorption.

Differential coupling between subcortical calcium and BOLD signals during evoked and resting state through simultaneous calcium fiber photometry and fMRI

Task based and resting state fMRI has been widely utilized to study brain functions. As the foundation of fMRI, the underlying neural basis of the BOLD signal has been extensively studied, but the detailed mechanism remains elusive, particularly during the resting state. To examine the neurovascular coupling, it is important to simultaneously record neural and vascular signals. Here we developed a novel setup of camera based, scalable simultaneous calcium fiber photometry and fMRI in rats. Using this setup, we recorded calcium signals of superior colliculus (SC) and lateral geniculate nucleus (LGN) and fMRI simultaneously during visual stimulation and the resting state. Our results revealed robust, region-specific coupling between calcium and BOLD signals in the task state and weaker, whole brain correlation in the resting state. Interestingly, the spatial specificity of such correlation in the resting state was improved upon regression of white matter, ventricle signals and global signals in fMRI data. Overall, our results suggest differential coupling of calcium and BOLD signals for subcortical regions between evoked and resting states, and the coupling relationship in the resting state was related with resting state BOLD preprocessing strategies.

Mesoscopic and microscopic imaging of sensory responses in the same animal

Imaging based on blood flow dynamics is widely used to study sensory processing. Here we investigated the extent to which local neuronal and capillary responses (two-photon microscopy) are correlated to mesoscopic responses detected with fast ultrasound (fUS) and BOLD-fMRI. Using a specialized chronic olfactory bulb preparation, we report that sequential imaging of the same mouse allows quantitative comparison of odour responses, imaged at both microscopic and mesoscopic scales. Under these conditions, functional hyperaemia occurred at the threshold of neuronal activation and fUS-CBV signals could be detected at the level of single voxels with activation maps varying according to blood velocity. Both neuronal and vascular responses increase non-linearly as a function of odour concentration, whereas both microscopic and mesoscopic vascular responses are linearly correlated to local neuronal calcium. These data establish strengths and limits of mesoscopic imaging techniques to report neural activity.

Neuronal activity leads to a local increase in blood flow and volume, a process termed hyperaemia. Here, the authors employ multiple imaging approaches of neuronal and vascular activity at varying resolution to delineate the spatiotemporal dynamics of neurovascular coupling evoked by odours in the olfactory bulb.

The Three-Dimensional Signal Collection Field for Fiber Photometry in Brain Tissue

Fiber photometry is used to monitor signals from fluorescent indicators in genetically-defined neural populations in behaving animals. Recently, fiber photometry has rapidly expanded and it now provides researchers with increasingly powerful means to record neural dynamics and neuromodulatory action. However, it is not clear how to select the optimal fiber optic given the constraints and goals of a particular experiment. Here, using combined confocal/2-photon microscope, we quantitatively characterize the fluorescence collection properties of various optical fibers in brain tissue. We show that the fiber size plays a major role in defining the volume of the optically sampled brain region, whereas numerical aperture impacts the total amount of collected signal and, marginally, the shape and size of the collection volume. We show that ~80% of the effective signal arises from 105 to 106 μm3 volume extending ~200 μm from the fiber facet for 200 μm core optical fibers. Together with analytical and ray tracing collection maps, our results reveal the light collection properties of different optical fibers in brain tissue, allowing for an accurate selection of the fibers for photometry and helping for a more precise interpretation of measurements in terms of sampled volume.

Multimodal Functional Neuroimaging by Simultaneous BOLD fMRI and Fiber-Optic Calcium Recordings and Optogenetic Control

Recent developments of optogenetic tools and fluorescence-based calcium recording techniques enable the manipulation and monitoring of neural circuits on a cellular level. Non-invasive imaging of brain networks, however, requires the application of methods such as blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI), which is commonly used for functional neuroimaging. While BOLD fMRI provides brain-wide non-invasive reading of the hemodynamic response, it is only an indirect measure of neural activity. Direct observation of neural responses requires electrophysiological or optical methods. The latter can be combined with optogenetic control of neuronal circuits and are MRI compatible. Yet, simultaneous optical recordings are still limited to fiber-optic-based approaches. Here, we review the integration of optical recordings and optogenetic manipulation into fMRI experiments. As a practical example, we describe how BOLD fMRI in a 9.4-T small animal MR scanner can be combined with in vivo fiber-optic calcium recordings and optogenetic control in a multimodal setup. We present simultaneous BOLD fMRI and calcium recordings under optogenetic control in rat. We outline details about MR coil configuration, choice, and usage of opsins and chemically and genetically encoded calcium sensors, fiber implantation, appropriate light power for stimulation, and calcium signal detection, to provide a glimpse into challenges and opportunities of this multimodal molecular neuroimaging approach.

Awake and behaving mouse fMRI during Go/No-Go task

Functional magnetic imaging (fMRI) has been widely used to examine the functional neural networks in both the evoked and resting states. However, most fMRI studies in rodents are performed under anesthesia, which greatly limits the scope of their application, and behavioral relevance. Efforts have been made to image rodents in the awake condition, either in the resting state or in response to sensory or optogenetic stimulation. However, fMRI in awake behaving rodents has not yet been achieved. In the current study, a novel fMRI paradigm for awake and behaving mice was developed, allowing functional imaging of the mouse brain in an olfaction-based go/no-go task. High resolution functional imaging with limited motion and image distortion were achieved at 9.4T with a cryogenic coil in awake and behaving mice. Distributed whole-brain spatiotemporal patterns were revealed, with drastically different activity profiles for go versus no-go trials. Therefore, we have demonstrated the feasibility of functional imaging of an olfactory behavior in awake mice. This fMRI paradigm in awake behaving mice could lead to novel insights into neural mechanisms underlying behaviors at a whole-brain level.

Tapered Fibers Combined With a Multi-Electrode Array for Optogenetics in Mouse Medial Prefrontal Cortex

Optogenetics offers many advantages in terms of cell-type specificity, allowing to investigate functional connectivity between different brain areas at high spatial and neural population selectivity. In order to obtain simultaneous optical control and electrical readout of neural activity, devices called "optrodes" are employed. They are typically composed of a linear array of microelectrodes integrated on a slender probe shafts combined with flat-cleaved optical fibers (FF) placed above the recording sites. However, due to tissue absorption and scattering, light delivered by the FF unevenly illuminates the region of interest. This issue is of particular relevance when cellular populations are disposed along the dorso-ventral axis, such as in medial prefrontal cortex (mPFC) where cortical layers are aligned vertically. The study presented here aims at using tapered optical fibers (TFs) in combination with a 16-electrode neural probe to better access neural populations distributed along the dorso-ventral axis in the mPFC of newborn mice, restricting light delivery over a specific portion of the cortical layer of interest. Half of the TF surface is coated with a reflecting metal blocking the light to enable light delivery from one side of the probe's shaft only, with the probe base being designed to host the fiber without interfering with the wire-bonds that connect the recording sites to a printed circuit board. Monte-Carlo simulations have been implemented to define the relative TF-probe position and to identify the light intensity distribution above the recording sites. In vivo recordings indicate that simultaneous optical stimulation and electrical readout of neural activity in the mPFC benefit from the use of the engineered TF-based optrode in terms of a more uniform light distribution along the dorso-ventral axis and the possibility of restricting light delivery to a subset of electrical recording sites of interest.

Optogenetic Modulation of a Minor Fraction of Parvalbumin-Positive Interneurons Specifically Affects Spatiotemporal Dynamics of Spontaneous and Sensory-Evoked Activity in Mouse Somatosensory Cortex in Vivo

Parvalbumin (PV) positive interneurons exert strong effects on the neocortical excitatory network, but it remains unclear how they impact the spatiotemporal dynamics of sensory processing in the somatosensory cortex. Here, we characterized the effects of optogenetic inhibition and activation of PV interneurons on spontaneous and sensory-evoked activity in mouse barrel cortex in vivo. Inhibiting PV interneurons led to a broad-spectrum power increase both in spontaneous and sensory-evoked activity. Whisker-evoked responses were significantly increased within 20 ms after stimulus onset during inhibition of PV interneurons, demonstrating high temporal precision of PV-shaped inhibition. Multiunit activity was strongly enhanced in neighboring cortical columns, but not at the site of transduction, supporting a central and highly specific role of PV interneurons in lateral inhibition. Inversely, activating PV interneurons drastically decreased spontaneous and whisker-evoked activity in the principal column and exerted strong lateral inhibition. Histological assessment of transduced cells combined with quantitative modeling of light distribution and spike sorting revealed that only a minor fraction (~10%) of the local PV population comprising no more than a few hundred neurons is optogenetically modulated, mediating the observed prominent and widespread effects on neocortical processing.

Fiber-optic implant for simultaneous fluorescence-based calcium recordings and BOLD fMRI in mice

Despite the growing popularity of blood oxygen level-dependent (BOLD) functional MRI (fMRI), understanding of its underlying principles is still limited. This protocol describes a technique for simultaneous measurement of neural activity using fluorescent calcium indicators together with the corresponding hemodynamic BOLD fMRI response in the mouse brain. Our early work using small-molecule fluorophores in rats gave encouraging results but was limited to acute measurements using synthetic dyes. Our latest procedure combines fMRI with optical detection of cell-type-specific virally delivered GCaMP6, a genetically encoded calcium indicator (GECI). GCaMP6 fluorescence, which increases upon calcium binding, is collected by a chronically implanted optical fiber, allowing longitudinal studies in mice. The chronic implant, placed horizontally on the skull, has an angulated tip that reflects light into the brain and is connected via fiber optics to a remote optical setup. The technique allows access to the neocortex and does not require adaptations of commercial MRI hardware. The hybrid approach permits fiber-optic calcium recordings with simultaneous artifact-free BOLD fMRI with full brain coverage and 1-s temporal resolution using standard gradient-echo echo-planar imaging (GE-EPI) sequences. The method provides robust, cell-type-specific readouts to link neural activity to BOLD signals, as emonstrated for task-free ('resting-state') conditions and in response to hind-paw stimulation. These results highlight the power of fiber photometry combined with fMRI, which we aim to further advance in this protocol. The approach can be easily adapted to study other molecular processes using suitable fluorescent indicators.

Cortex-wide BOLD fMRI activity reflects locally-recorded slow oscillation-associated calcium waves

Spontaneous slow oscillation-associated slow wave activity represents an internally generated state which is characterized by alternations of network quiescence and stereotypical episodes of neuronal activity - slow wave events. However, it remains unclear which macroscopic signal is related to these active periods of the slow wave rhythm. We used optic fiber-based calcium recordings of local neural populations in cortex and thalamus to detect neurophysiologically defined slow calcium waves in isoflurane anesthetized rats. The individual slow wave events were used for an event-related analysis of simultaneously acquired whole-brain BOLD fMRI. We identified BOLD responses directly related to onsets of slow calcium waves, revealing a cortex-wide BOLD correlate: the entire cortex was engaged in this specific type of slow wave activity. These findings demonstrate a direct relation of defined neurophysiological events to a specific BOLD activity pattern and were confirmed for ongoing slow wave activity by independent component and seed-based analyses.

When a person is in a deep non-dreaming sleep, neurons in their brain alternate slowly between periods of silence and periods of activity. This gives rise to low-frequency brain rhythms called slow waves, which are thought to help stabilize memories. Slow wave activity can be detected on multiple scales, from the pattern of electrical impulses sent by an individual neuron to the collective activity of the brain’s entire outer layer, the cortex. But does slow wave activity in an individual group of neurons in the cortex affect the activity of the rest of the brain?

To find out, Schwalm, Schmid, Wachsmuth et al. took advantage of the fact that slow waves also occur under general anesthesia, and placed anesthetized rats inside miniature whole-brain scanners. A small region of cortex in each rat had been injected with a dye that fluoresces whenever the neurons in that region are active. An optical fiber was lowered into the rat’s brain to transmit the fluorescence signals to a computer. Monitoring these signals while the animals lay inside the scanner revealed that slow-wave activity in any one group of cortical neurons was accompanied by slow-wave activity across the cortex as a whole. This relationship was seen only for slow waves, and not for other brain rhythms.

Slow waves seem to occur in all species of animal with a backbone, and in both healthy and diseased brains. While it is not possible to inject fluorescent dyes into the human brain, it is possible to monitor neuronal activity using electrodes. Comparing local electrode recordings with measures of whole-brain activity from scanners could thus allow similar experiments to be performed in people. There is growing evidence – from animal models and from studies of patients – that slow waves may be altered in Alzheimer’s disease. Further work is required to determine whether detecting these changes could help diagnose disease at earlier stages, and whether reversing them may have therapeutic potential.

Simultaneous GCaMP6-based fiber photometry and fMRI in rats

BACKGROUND

Understanding the relationship between neural and vascular signals is essential for interpretation of functional MRI (fMRI) results with respect to underlying neuronal activity. Simultaneously measuring neural activity using electrophysiology with fMRI has been highly valuable in elucidating the neural basis of the blood oxygenation-level dependent (BOLD) signal. However, this approach is also technically challenging due to the electromagnetic interference that is observed in electrophysiological recordings during MRI scanning.

NEW METHOD

Recording optical correlates of neural activity, such as calcium signals, avoids this issue, and has opened a new avenue to simultaneously acquire neural and BOLD signals.

RESULTS

The present study is the first to demonstrate the feasibility of simultaneously and repeatedly acquiring calcium and BOLD signals in animals using a genetically encoded calcium indicator, GCaMP6. This approach was validated with a visual stimulation experiment, during which robust increases of both calcium and BOLD signals in the superior colliculus were observed. In addition, repeated measurement in the same animal demonstrated reproducible calcium and BOLD responses to the same stimuli.

COMPARISON WITH EXISTING METHOD(S)

Taken together, simultaneous GCaMP6-based fiber photometry and fMRI recording presents a novel, artifact-free approach to simultaneously measuring neural and fMRI signals. Furthermore, given the cell-type specificity of GCaMP6, this approach has the potential to mechanistically dissect the contributions of individual neuron populations to BOLD signal, and ultimately reveal its underlying neural mechanisms.

CONCLUSIONS

The current study established the method for simultaneous GCaMP6-based fiber photometry and fMRI in rats.

From unspecific to adjusted, how the BOLD response in the rat hippocampus develops during consecutive stimulations

To determine the possibility to deconvolve measured BOLD responses to neuronal signals, the rat perforant pathway was electrically stimulated with 10 related stimulation protocols. All stimulation protocols were composed of low-frequency pulse sequences with superimposed high-frequency pulse bursts. Because high-frequency pulse bursts trigger only one synchronized spiking of granular cells, variations of the stimulation protocol were used: (a) to keep the spiking activity similar during the presentation of different numbers of pulses, (b) to apply identical numbers of pulses to induce different amounts of spiking activity, and (c) to concurrently vary the number of applied electrical pulses and resultant spiking activity. When complex pulse sequences enter the hippocampus, an unspecific default-like BOLD response is first generated, which relates neither to the number of incoming pulses nor to the induced spiking activity. Only during subsequent stimulations does the initial unspecific response adjust to a more adequate response, which in turn either strongly related to spiking activity when low-frequency pulses were applied or depended on the incoming activity when high-frequency pulse bursts were presented. Thus, only the development of BOLD responses during repetitive stimulations can predict the underlying neuronal activity and deconvolution analysis should not be performed during an initial stimulation period.

Blood oxygenation level dependent signal and neuronal adaptation to optogenetic and sensory stimulation in somatosensory cortex in awake animals

The adaptation of neuronal responses to stimulation, in which a peak transient response is followed by a sustained plateau, has been well-studied. The blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) signal has also been shown to exhibit adaptation on a longer time scale. However, some regions such as the visual and auditory cortices exhibit significant BOLD adaptation, whereas other such as the whisker barrel cortex may not adapt. In the sensory cortex a combination of thalamic inputs and intracortical activity drives hemodynamic changes, although the relative contributions of these components are not entirely understood. The aim of this study is to assess the role of thalamic inputs vs. intracortical processing in shaping BOLD adaptation during stimulation in the somatosensory cortex. Using simultaneous fMRI and electrophysiology in awake rabbits, we measured BOLD, local field potentials (LFPs), single- and multi-unit activity in the cortex during whisker and optogenetic stimulation. This design allowed us to compare BOLD and haemodynamic responses during activation of the normal thalamocortical sensory pathway (i.e., both inputs and intracortical activity) vs. the direct optical activation of intracortical circuitry alone. Our findings show that whereas LFP and multi-unit (MUA) responses adapted, neither optogenetic nor sensory stimulation produced significant BOLD adaptation. We observed for both paradigms a variety of excitatory and inhibitory single unit responses. We conclude that sensory feed-forward thalamic inputs are not primarily responsible for shaping BOLD adaptation to stimuli; but the single-unit results point to a role in this behaviour for specific excitatory and inhibitory neuronal sub-populations, which may not correlate with aggregate neuronal activity.

True and apparent optogenetic BOLD fMRI signals

PURPOSE

Optogenetic fMRI (ofMRI) is a novel tool in neurophysiology and neuroimaging. The method is prone to light-induced artifacts, two of which were investigated in this study.

METHODS

ofMRI was performed in rats using two excitatory opsins (ChR2 and C1V1_TT ) virally transduced in somatosensory cortex or thalamus. Heat-induced apparent BOLD activation at the site of the optical fiber and stimulation light-induced activation of the visual pathways were investigated, and control experiments for these two artifacts were established.

RESULTS

Specific optogenetic BOLD activation was observed with both opsins, accompanied by BOLD in the visual pathways. Unspecific heat-induced BOLD was ruled out by a control experiment employing low-level constant illumination in addition to pulsed optogenetic stimulation. Activation of the visual pathways was confirmed to be physiological by direct visual stimulation of the eyes and was suppressed by additional low-level constant light to the eyes. Light inside the brain was identified as one source of the BOLD signal observed in the visual pathways.

CONCLUSION

ofMRI is a method of tremendous potential, but unspecific activations in fMRI not caused by the activation of opsins must be avoided or recognized as such. The control experiments presented here allow for validating the specificity of optogenetic stimulation. Magn Reson Med 77:126-136, 2017. © 2016 Wiley Periodicals, Inc.