Functional Magnetic Resonance Imaging (fMRI) in awake behaving mice is well positioned to bridge the detailed cellular-level view of brain activity, which has become available due to recent advances in microscopic optical imaging and genetics, to the macroscopic scale of human noninvasive observables. Here, we demonstrate Blood Oxygen Level Dependent (BOLD) fMRI in awake mice implanted with chronic transparent cranial ''windows'', compatible with two-photon microscopy, optical imaging, and optogenetic light stimulation. We thus provide a proof of feasibility for multimodal imaging approaches in awake mice, which in the future can be extended to behavioral studies and biomedical applications.
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