Graph-based unsupervised segmentation algorithm for cultured neuronal networks' structure characterization and modeling

Daniel de Santos-Sierra*, Irene Sendiña-Nadal, Inmaculada Leyva, Juan A. Almendral, Amir Ayali, Sarit Anava, Carmen Sánchez-Ávila, Stefano Boccaletti

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Large scale phase-contrast images taken at high resolution through the life of a cultured neuronal network are analyzed by a graph-based unsupervised segmentation algorithm with a very low computational cost, scaling linearly with the image size. The processing automatically retrieves the whole network structure, an object whose mathematical representation is a matrix in which nodes are identified neurons or neurons' clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocytochemistry techniques, our non invasive measures entitle us to perform a longitudinal analysis during the maturation of a single culture. Such an analysis furnishes the way of individuating the main physical processes underlying the self-organization of the neurons' ensemble into a complex network, and drives the formulation of a phenomenological model yet able to describe qualitatively the overall scenario observed during the culture growth.

Original languageEnglish
Pages (from-to)513-523
Number of pages11
JournalCytometry. Part A : the journal of the International Society for Analytical Cytology
Issue number6
StatePublished - 1 Jun 2015


  • Automated tracing
  • Complex networks
  • Connectome reconstruction
  • Cultured neuronal network
  • High throughput
  • Light microscopy
  • Network topology analysis
  • Neurite tracing
  • Neuron image segmentation
  • Neuronal morphology


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