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Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods
Alexander Song1, Jeff L Gauthier2, Jonathan W Pillow3
1Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Physics, Princeton University, Princeton, 08540 NJ, USA.
Journal of Neuroscience Methods
|April 11, 2021
Summary
A new simulation framework, Neural Anatomy and Optical Microscopy (NAOMi), enables robust validation of in vivo functional imaging techniques. This tool allows direct comparison of optical microscopy methods and algorithms for improved neural imaging research.
Area of Science:
- Neuroscience
- Optical Microscopy
- Computational Biology
Background:
- The rapid development of in vivo functional imaging techniques necessitates rigorous validation.
- Lack of standardized evaluation metrics hinders the systematic assessment of optical microscopy methods.
Purpose of the Study:
- To introduce a novel computational framework, NAOMi, for evaluating two-photon microscopy.
- To provide a ground-truth resource for comparing different imaging and analysis approaches.
Main Methods:
- Developed NAOMi, a computationally efficient simulation framework for mouse cortex.
- Simulated neural activity, optical propagation, and scanning to generate realistic calcium imaging data.
- Validated NAOMi against in vivo two-photon recordings.
Main Results:
- NAOMi simulations accurately replicate in vivo two-photon recordings.
- Modern segmentation algorithms show high performance but increased false positives.
- Bessel beams improve motion artifact resilience; Gaussian beams enhance signal-to-noise ratio; temporal focusing offers uniform sampling.
Conclusions:
- NAOMi is the first framework for assessing functional optical microscopy modalities.
- The framework leverages anatomical and optical knowledge to advance neural imaging method development.
- NAOMi provides a powerful tool for the assessment and development of neural imaging techniques.
