Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI

Nat Methods. 2020 Dec;17(12):1262-1271. doi: 10.1038/s41592-020-00984-6. Epub 2020 Nov 2.


Achieving a comprehensive understanding of brain function requires multiple imaging modalities with complementary strengths. We present an approach for concurrent widefield optical and functional magnetic resonance imaging. By merging these modalities, we can simultaneously acquire whole-brain blood-oxygen-level-dependent (BOLD) and whole-cortex calcium-sensitive fluorescent measures of brain activity. In a transgenic murine model, we show that calcium predicts the BOLD signal, using a model that optimizes a gamma-variant transfer function. We find consistent predictions across the cortex, which are best at low frequency (0.009-0.08 Hz). Furthermore, we show that the relationship between modality connectivity strengths varies by region. Our approach links cell-type-specific optical measurements of activity to the most widely used method for assessing human brain function.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Blood Gas Analysis
  • Brain Mapping / methods*
  • Calcium / metabolism
  • Calcium-Binding Proteins / genetics
  • Calcium-Binding Proteins / metabolism*
  • Cerebral Cortex / diagnostic imaging*
  • Fluorescence
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • Magnetic Resonance Imaging / methods*
  • Mice
  • Mice, Transgenic
  • Oxygen / analysis


  • Calcium-Binding Proteins
  • Green Fluorescent Proteins
  • Oxygen
  • Calcium