Abstract
Sleep is an essential process for the survival of animals. However, its phenomenon is poorly understood. To understand the phenomenon of sleep, the analysis should be made from the activities of a large number of cortical neurons. Calcium imaging is a recently developed technique that can record a large number of neurons simultaneously, however, it has a disadvantage of low time resolution. In this paper, we aim to discover phenomena which characterize sleep/wake states from calcium imaging data. We made an assumption that groups of neurons become active simultaneously and the neuronal activities of groups differ between sleep and wake states. We used non-negative matrix factorization (NMF) to identify those groups and their neuronal activities in time from calcium imaging data. NMF was used because neural activity can be expressed by the sum of individual neuronal activity and fluorescence intensity data are always positive values. We found that there are certain groups of neurons that behave differently between sleep and wake states.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Breiman, L.: Random forests. Mach. Learn. 45(1), 5–32 (2001). https://doi.org/10.1023/A:1010933404324
Chen, T.W., et al.: Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499(7458), 295–300 (2013). https://doi.org/10.1038/nature12354
Cichocki, A., Zdunek, R., Phan, A.H., Amari, S.: Nonnegative Matrix and Tensor Factorizations. Wiley, Chichester (2009)
Cox, J., Pinto, L., Dan, Y.: Calcium imaging of sleep-wake related neuronal activity in the dorsal pons. Nat. Commun. 7(1), 10763 (2016). https://doi.org/10.1038/ncomms10763
Dayan, E., Cohen, L.G.: Neuroplasticity subserving motor skill learning. Neuron 72(3), 443–54 (2011). https://doi.org/10.1016/j.neuron.2011.10.008
Deboer, T.: Technologies of sleep research. Cell. Mol. Life Sci. 64(10), 1227 (2007). https://doi.org/10.1007/s00018-007-6533-0
Dombeck, D.A., Graziano, M.S., Tank, D.W.: Functional clustering of neurons in motor cortex determined by cellular resolution imaging in awake behaving mice. J. Neurosci. 29(44), 13751–13760 (2009). https://doi.org/10.1523/JNEUROSCI.2985-09.2009
Evarts, E.V.: Temporal patterns of discharge of pyramidal tract neurons during sleep and waking in the monkey. J. Neurophys. 27, 152–71 (1964). https://doi.org/10.1152/jn.1964.27.2.152
Hobson, J.A.: Sleep is of the brain, by the brain and for the brain. Nature 437(7063), 1254–1256 (2005). https://doi.org/10.1038/nature04283
Kanda, T., et al.: Sleep as a biological problem: an overview of frontiers in sleep research. J. Physiol. Sci. 66(1), 1–13 (2016). https://doi.org/10.1007/s12576-015-0414-3
Lee, D.D., Seung, H.S.: Learning the parts of objects by non-negative matrix factorization. Nature 401(6755), 788–791 (1999). https://doi.org/10.1038/44565
Lin, J.: Divergence measures based on the Shannon entropy. IEEE Trans. Inform. Theory 37(1), 145–151 (1991). https://doi.org/10.1109/18.61115
Mishchencko, Y., Vogelstein, J.T., Paninski, L.: A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data. Ann. Appl. Stat. 5(2B), 1229–1261 (2011). https://doi.org/10.1214/09-AOAS303
Peters, A.J., Chen, S.X., Komiyama, T.: Emergence of reproducible spatiotemporal activity during motor learning. Nature 510(7504), 263–267 (2014). https://doi.org/10.1038/nature13235
Sjulson, L., Miesenböck, G.: Optical recording of action potentials and other discrete physiological events: a perspective from signal detection theory. Physiology 22(1), 47–55 (2007). https://doi.org/10.1152/physiol.00036.2006
Vogelstein, J.T., Watson, B.O., Packer, A.M., Yuste, R., Jedynak, B., Paninski, L.: Spike inference from calcium imaging using sequential Monte Carlo methods. Biophys. J. 97(2), 636–655 (2009). https://doi.org/10.1016/J.BPJ.2008.08.005
Acknowledgements
This work was supported by Grants-in-Aid for Scientific Research (KAKENHI), Japan Society for the Promotion of Science (JSPS) (Grant Number 16K18358 to T.K.; 26220207 to T.K. and M.Y.; 19K12111 to H.H; 17H06095 to M.Y.); World Premier International Research Center Initiative (WPI), the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (to M.Y.); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST) (Grant Number JPMJCR1761 to H.H.; JPMJCR1655 to M.Y.); Yamada Research Grant (to T.K.), Takeda Science Foundation (to M.Y.), and Uehara Memorial Foundation (to M.Y.).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Nagayama, M. et al. (2019). Sleep State Analysis Using Calcium Imaging Data by Non-negative Matrix Factorization. In: Tetko, I., Kůrková, V., Karpov, P., Theis, F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Theoretical Neural Computation. ICANN 2019. Lecture Notes in Computer Science(), vol 11727. Springer, Cham. https://doi.org/10.1007/978-3-030-30487-4_8
Download citation
DOI: https://doi.org/10.1007/978-3-030-30487-4_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-30486-7
Online ISBN: 978-3-030-30487-4
eBook Packages: Computer ScienceComputer Science (R0)