Detecting cells using non-negative matrix factorization on calcium imaging data

Neural Netw. 2014 Jul;55:11-9. doi: 10.1016/j.neunet.2014.03.007. Epub 2014 Mar 24.


We propose a cell detection algorithm using non-negative matrix factorization (NMF) on Ca2+ imaging data. To apply NMF to Ca2+ imaging data, we use the bleaching line of the background fluorescence intensity as an a priori background constraint to make the NMF uniquely dissociate the background component from the image data. This constraint helps us to incorporate the effect of dye-bleaching and reduce the non-uniqueness of the solution. We demonstrate that in the case of noisy data, the NMF algorithm can detect cells more accurately than Mukamel's independent component analysis algorithm, a state-of-art method. We then apply the NMF algorithm to Ca2+ imaging data recorded on the local activities of subcellular structures of multiple cells in a wide area. We show that our method can decompose rapid transient components corresponding to somas and dendrites of many neurons, and furthermore, that it can decompose slow transient components probably corresponding to glial cells.

Keywords: Dendrite; Independent component analysis; Multi-cellular calcium imaging; Non-negative matrix factorization; Semi-automatic cell detection.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • CA1 Region, Hippocampal / cytology*
  • Calcium / analysis*
  • Computer Simulation
  • Dendrites / chemistry
  • Male
  • Models, Neurological*
  • Neurons / chemistry*
  • Neurons / cytology
  • Rats
  • Rats, Wistar
  • Reproducibility of Results


  • Calcium