Automated sleep state classification of wide-field calcium imaging data via multiplex visibility graphs and deep learning

Xiaohui Zhang, Eric C. Landsness, Wei Chen, Hanyang Miao, Michelle Tang, Lindsey M. Brier, Joseph P. Culver, Jin Moo Lee, Mark A. Anastasio

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


Background: Wide-field calcium imaging (WFCI) allows for monitoring of cortex-wide neural dynamics in mice. When applied to the study of sleep, WFCI data are manually scored into the sleep states of wakefulness, non-REM (NREM) and REM by use of adjunct EEG and EMG recordings. However, this process is time-consuming and often suffers from low inter- and intra-rater reliability and invasiveness. Therefore, an automated sleep state classification method that operates on WFCI data alone is needed. New method: A hybrid, two-step method is proposed. In the first step, spatial-temporal WFCI data is mapped to multiplex visibility graphs (MVGs). Subsequently, a two-dimensional convolutional neural network (2D CNN) is employed on the MVGs to be classified as wakefulness, NREM and REM. Results: Sleep states were classified with an accuracy of 84% and Cohen's κ of 0.67. The method was also effectively applied on a binary classification of wakefulness/sleep (accuracy=0.82, κ = 0.62) and a four-class wakefulness/sleep/anesthesia/movement classification (accuracy=0.74, κ = 0.66). Gradient-weighted class activation maps revealed that the CNN focused on short- and long-term temporal connections of MVGs in a sleep state-specific manner. Sleep state classification performance when using individual brain regions was highest for the posterior area of the cortex and when cortex-wide activity was considered. Comparison with existing method: On a 3-hour WFCI recording, the MVG-CNN achieved a κ of 0.65, comparable to a κ of 0.60 corresponding to the human EEG/EMG-based scoring. Conclusions: The hybrid MVG-CNN method accurately classifies sleep states from WFCI data and will enable future sleep-focused studies with WFCI.

Original languageEnglish
Article number109421
JournalJournal of Neuroscience Methods
StatePublished - Jan 15 2022


  • 2D CNN
  • Automated sleep state classification
  • Deep learning
  • Local sleep
  • Multiplex visibility graph
  • Wide-field calcium imaging


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