ArticleNature communications2022
A deep-learning approach for online cell identification and trace extraction in functional two-photon calcium imaging.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 68 citations in OpenAlex.
- Celldetective, an AI-enhanced image analysis tool for unraveling dynamic cell interactions.eLife · 2026Article
- NeuroSeg-MF: robust neuron segmentation in two-photon CaBiomedical optics express · 2026Article
- Optimization of spatial and temporal sampling resolution for optophysiology in large-scale two-photon calcium imaging.Biomedical optics express · 2026Article
- Next-generation multicolor indicators for in vivo imaging of norepinephrine.Nature methods · 2026Article
- Combinatorial responsiveness of chemosensory neurons in mouse explants revealed by DynamicNeuroTracker.Cell reports methods · 2025Article
- A Semi-Automatic Tool for the Standardized Analysis of Fluorescent Intensity Changes in Polarized Cells.International journal of molecular sciences · 2025Article
- DeepInMiniscope: Deep learning-powered physics-informed integrated miniscope.Science advances · 2025Article
- Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae.iScience · 2025Article
- CalTrig: A GUI-Based Machine Learning Approach for Decoding Neuronal Calcium Transients in Freely Moving Rodents.eNeuro · 2025Article
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- Window into the Brain: In Vivo Multiphoton Imaging.ACS photonics · 2025Review
- A generative benchmark for evaluating the performance of fluorescent cell image segmentation.Synthetic and systems biotechnology · 2024Article
- CalTrig: A GUI-based Machine Learning Approach for Decoding Neuronal Calcium Transients in Freely Moving Rodents.bioRxiv : the preprint server for biology · 2024Article
- Article
- An end-to-end recurrent compressed sensing method to denoise, detect and demix calcium imaging data.Nature machine intelligence · 2024Article
- Closed-loop experiments and brain machine interfaces with multiphoton microscopy.Neurophotonics · 2024Review
- NeuroSeg-III: efficient neuron segmentation in two-photon CaBiomedical optics express · 2024Article
- ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface.Bioinformatics (Oxford, England) · 2024Article
- Wireless closed-loop deep brain stimulation using microelectrode array probes.Journal of Zhejiang University. Science. B · 2024Review
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
In vivo two-photon calcium imaging is a powerful approach in neuroscience. However, processing two-photon calcium imaging data is computationally intensive and time-consuming, making online frame-by-frame analysis challenging. This is especially true for large field-of-view (FOV) imaging. Here, we present CITE-On (Cell Identification and Trace Extraction Online), a convolutional neural network-based algorithm for fast automatic cell identification, segmentation, identity tracking, and trace extraction in two-photon calcium imaging data. CITE-On processes thousands of cells online, including during mesoscopic two-photon imaging, and extracts functional measurements from most neurons in the FOV. Applied to publicly available datasets, the offline version of CITE-On achieves performance similar to that of state-of-the-art methods for offline analysis. Moreover, CITE-On generalizes across calcium indicators, brain regions, and acquisition parameters in anesthetized and awake head-fixed mice. CITE-On represents a powerful tool to speed up image analysis and facilitate closed-loop approaches, for example in combined all-optical imaging and manipulation experiments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.