Studying the physiological impact of transcranial ultrasound in rodent brains may offer an important preclinical model for human scale magnetic resonance-guided focused ultrasound methods. Therefore, this study found a versatile bidirectional hybrid fluorescence-ultrasound system with a fiberscope-based wide-field fluorescence imaging. This dataset contains functional connectivity data. The functional connectivity data includes connectivity matrices before and after sonication with a single 100 ms 3.9 MPa pulse and 150 ms 3 MPa pulse delivered 20 times. The dataset also contains image data of vessels and astrocytes after single 3.9 MPa sonication, microglia after single 3.9 MPa sonication, and lesion after single 4.5 MPa sonication. This data indicate that cortex-wide functional imaging and targeted ultrasound delivery can be used to transcranially map previously undocumented localized fluorescence events.