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Neural Anatomy and Optical Microscopy (NAOMi) Simulation Translation for Increased Efficiency and Accessibility to Ground-truth Calcium Imaging Data

Team Members:
  • Marianna Elia
  • Kangjia Cai
  • Ryan Zhao
  • Zhining Chen
  • Adam Charles


The Neural Anatomy and Optical Microscopy (NAOMi) is a first-in-class approach in that it is the only existing framework for simulating functional optical microscopy data. It was developed to tackle the lack of ground-truth comparisons or evaluation metrics in optical microscopy of neural tissue.

In this project, we mainly focus on translating the NAOMi codebase from MATLAB to Python in order to increase the accessibility of the simulation as well as optimize it for both speed and memory. We also hope to update the documentation of the codebase so that it is clear and concise. It is expected that a working Python codebase for the four main sub-function will be available by the end of this project with updated code documentation to alleviate difficulties for later code maintenance and modifications.‚Äč

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