A deep-learning approach for online cell identification and trace extraction in functional two-photon calcium imaging.
Luca SitàMarco BrondiPedro Lagomarsino de Leon RoigSebastiano CurreliMariangela PannielloDania VecchiaTommaso FellinPublished in: Nature communications (2022)
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.
Keyphrases
- high resolution
- deep learning
- convolutional neural network
- single cell
- machine learning
- type diabetes
- spinal cord injury
- living cells
- cell therapy
- healthcare
- stem cells
- metabolic syndrome
- skeletal muscle
- artificial intelligence
- signaling pathway
- bone marrow
- mass spectrometry
- rna seq
- cell death
- optical coherence tomography
- deep brain stimulation
- high speed
- insulin resistance
- monte carlo