Detecting neural assemblies in calcium imaging data

Jan Mölter, Lilach Avitan, Geoffrey J. Goodhill*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


Background: Activity in populations of neurons often takes the form of assemblies, where specific groups of neurons tend to activate at the same time. However, in calcium imaging data, reliably identifying these assemblies is a challenging problem, and the relative performance of different assembly-detection algorithms is unknown. Results: To test the performance of several recently proposed assembly-detection algorithms, we first generated large surrogate datasets of calcium imaging data with predefined assembly structures and characterised the ability of the algorithms to recover known assemblies. The algorithms we tested are based on independent component analysis (ICA), principal component analysis (Promax), similarity analysis (CORE), singular value decomposition (SVD), graph theory (SGC), and frequent item set mining (FIM-X). When applied to the simulated data and tested against parameters such as array size, number of assemblies, assembly size and overlap, and signal strength, the SGC and ICA algorithms and a modified form of the Promax algorithm performed well, while PCA-Promax and FIM-X did less well, for instance, showing a strong dependence on the size of the neural array. Notably, we identified additional analyses that can improve their importance. Next, we applied the same algorithms to a dataset of activity in the zebrafish optic tectum evoked by simple visual stimuli, and found that the SGC algorithm recovered assemblies closest to the averaged responses. Conclusions: Our findings suggest that the neural assemblies recovered from calcium imaging data can vary considerably with the choice of algorithm, but that some algorithms reliably perform better than others. This suggests that previous results using these algorithms may need to be reevaluated in this light.

Original languageAmerican English
Article number143
JournalBMC Biology
Issue number1
StatePublished - 28 Nov 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).


  • Clustering
  • Population coding
  • Spontaneous activity


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