Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods
Authors: Alexander Song, Jeff L. Gauthier, Jonathan W. Pillow, David W. Tank, Adam S. Charles
PUBLIcation: Journal of neuroscience methods 2021
Background
The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes the large-scale, systematic validation vital to the continued development and use of optical microscopy impossible.
New-method
We provide a new framework for evaluating two-photon microscopy methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation. Our computationally efficient model generates large anatomical volumes of mouse cortex, simulates neural activity, and incorporates optical propagation and scanning to create realistic calcium imaging datasets.