Simultaneous optical imaging and fMRI: Examining concert neural activity in the cortex and the whole brain BOLD signal

A wide array of neuroimaging tools exists, each with its own set of tradeoffs. By combining complementary methods with different strengths and weaknesses, we can gain deeper insight into the measurements we obtain, and the organizational principles that govern brain function in health and disease.
Published in Protocols & Methods
Simultaneous optical imaging and fMRI: Examining concert neural activity in the cortex and the whole brain BOLD signal

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This work is the culmination of a highly innovative and interdisciplinary effort to span spatiotemporal scales from the micro to macroscopic [1]. Despite the scientific advances to be made by multi-modal imaging, for many methods, their combination has been hindered by unsolved technical challenges. Here, we present an approach that enable us to perform simultaneous mesoscopic calcium (Ca2+) imaging and functional magnetic resonance imaging (functional MRI, or fMRI).

Functional MRI provides a non-invasive measure of brain activity in both humans and animals with whole-brain coverage, making it a prominent tool in neuroscience. However, fMRI has relatively low spatial and temporal resolution, and relies on an indirect and cell type indiscriminate index of activity through a blood oxygen level dependent (BOLD) contrast mechanism [2]. The BOLD signal is complex and difficult to interpret - therefore a better understanding of the cellular origins of the BOLD signal stands to have a major impact on the field.

Recent advances have enabled the introduction of genetically encoded or virally mediated Ca2+ indicators that report on the activity of targeted cell types through the emission of a fluorescence signal. With this approach, we can use wide field or “mesoscopic” fluorescence imaging to measure swaths of cortical activity at high spatial and temporal resolution, and with cell type specificity [3]. However, Ca2+ imaging is limited to optically accessible tissue, and the expression of Ca2+ indicators necessitates invasive manipulation of the nervous system, limiting the practical application of this methodology to animal models.

Functional MRI and mesoscopic Ca2+ imaging are two highly complementary neuroimaging methods. Outside of the MRI scanner, mesoscopic Ca2+ imaging data are acquired from a head-fixed subject using a light source and camera located directly above the animal. The confined space, and high magnetic field of the MRI system are not conducive to within scanner mesoscopic Ca2+ signal recordings without major hardware alterations. Further, the MRI hardware limits optical access to the cortical surface, and vibrations caused by MR signal acquisition make combining these measures very challenging. To overcome these obstacles, we developed novel optical and MRI hardware, software (for multi-modal data analyses), and surgical procedures.

To successfully perform simultaneous mesoscopic Ca2+ and fMR imaging, we designed and built an MR-compatible optical device which enables fluorescence signal recording within the magnet. A key feature of this device is a 15-foot fiber optic bundle (containing over two million fibers) that allows us to relay mesoscopic Ca2+ imaging data from within the MRI scanner to an adjacent room where the camera, light source, and computer can be safely housed. In this work, we describe these developments and demonstrate the high-performance capabilities of our device.

Despite widespread use, the interpretation of fMRI data is hindered by our limited understanding of the physiological events which give rise to the BOLD signal. Simultaneous mesoscopic Ca2+ imaging offers a means of investigating the cell type specific underpinnings of the BOLD signal. Our multi-modal imaging approach will improve our biological understanding of BOLD signal origins in health and disease.


  1. Barson, D. et al. Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits. Nat Methods 17, 107-113 (2020).
  2. Ogawa, S. et al. Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proc Natl Acad Sci USA, 87, 9868-9872 (1990).
  3. Ross, WN. Understanding calcium waves and sparks in central neurons. Nat Rev Neurosci 13, 157-168 (2012).

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Biological Techniques
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