ArticleJournal of neuroscience methods2021
Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods.
Article in Journal of neuroscience methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 70 citations in OpenAlex.
- Rapid robust high-fidelity 3D neuronal extraction from multiview calcium imaging datasets.Nature methods · 2026Article
- High-fidelity fast fluorescence lifetime imaging by event-based denoising.Nature biotechnology · 2026Article
- High-fidelity intravital imaging of biological dynamics with latent-space-enhanced digital adaptive optics.Nature biotechnology · 2026Article
- Bridging Model and Experiment in Systems Neuroscience with Cleo: The Closed-Loop, Electrophysiology, and Optophysiology Simulation Testbed.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Combinatorial responsiveness of chemosensory neurons in mouse explants revealed by DynamicNeuroTracker.Cell reports methods · 2025Article
- Improved inference of latent neural states from calcium imaging data.bioRxiv : the preprint server for biology · 2025Article
- Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed.bioRxiv : the preprint server for biology · 2025Article
- Cognitive processes are disentangled at cortex-wide scales.bioRxiv : the preprint server for biology · 2025Article
- Unraveling the neural code: analysis of large-scale two-photon microscopy data.Microscopy (Oxford, England) · 2025Review
- Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis.PLoS computational biology · 2025Article
- Real-time and universal network for volumetric imaging from microscale to macroscale at high resolution.Light, science & applications · 2025Article
- An end-to-end recurrent compressed sensing method to denoise, detect and demix calcium imaging data.Nature machine intelligence · 2024Article
- Article
- Accurate neuron segmentation method for one-photon calcium imaging videos combining convolutional neural networks and clustering.Communications biology · 2024Article
- Simultaneous removal of noise and correction of motion warping in neuron calcium imaging using a pipeline structure of self-supervised deep learning models.Biomedical optics express · 2024Article
- A miniaturized mesoscope for the large-scale single-neuron-resolved imaging of neuronal activity in freely behaving mice.Nature biomedical engineering · 2024Article
- ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface.Bioinformatics (Oxford, England) · 2024Article
- Advances in cellular resolution microscopy for brain imaging in rats.Neurophotonics · 2023Review
- Statistically unbiased prediction enables accurate denoising of voltage imaging data.Nature methods · 2023Article
- Addressing annotation and data scarcity when designing machine learning strategies for neurophotonics.Neurophotonics · 2023Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe 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-
methodWe 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.
resultsWe verify NAOMi simulations against in vivo two-photon recordings from mouse cortex. We leverage this in silico ground truth to directly compare different segmentation algorithms and optical designs. We find modern segmentation algorithms extract strong neural time-courses comparable to estimation using oracle spatial information, but with an increase in the false positive rate. Comparison between optical setups demonstrate improved resilience to motion artifacts in sparsely labeled samples using Bessel beams, increased signal-to-noise ratio and cell-count using low numerical aperture Gaussian beams and nuclear GCaMP, and more uniform spatial sampling with temporal focusing versus multi-plane imaging. COMPARISON WITH EXISTING
methodsNAOMi is a first-of-its kind framework for assessing optical imaging modalities. Existing methods are either anatomical simulations or do not address functional imaging. Thus there is no competing method for simulating realistic functional optical microscopy data.
conclusionsBy leveraging the rich accumulated knowledge of neural anatomy and optical physics, we provide a powerful new tool to assess and develop important methods in neural imaging.
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