Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration

Commun Biol. 2019 May 1;2:155. doi: 10.1038/s42003-019-0411-9. eCollection 2019.


Current approaches for dynamic profiling of single cells rely on dissociated cultures, which lack important biological features existing in tissues. Organotypic slice cultures preserve aspects of structural and synaptic organisation within the brain and are amenable to microscopy, but established techniques are not well adapted for high throughput or longitudinal single cell analysis. Here we developed a custom-built, automated confocal imaging platform, with improved organotypic slice culture and maintenance. The approach enables fully automated image acquisition and four-dimensional tracking of morphological changes within individual cells in organotypic cultures from rodent and human primary tissues for at least 3 weeks. To validate this system, we analysed neurons expressing a disease-associated version of huntingtin (HTT586Q138-EGFP), and observed that they displayed hallmarks of Huntington's disease and died sooner than controls. By facilitating longitudinal single-cell analyses of neuronal physiology, our system bridges scales necessary to attain statistical power to detect developmental and disease phenotypes.

Keywords: Animal disease models; Confocal microscopy; Neurodegeneration; Time-lapse imaging; Tissue culture.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Substitution
  • Animals
  • Animals, Newborn
  • Cell Differentiation
  • Cell Tracking / instrumentation
  • Cell Tracking / methods*
  • Gene Expression
  • Hippocampus / metabolism
  • Hippocampus / pathology
  • Hippocampus / ultrastructure*
  • Humans
  • Huntingtin Protein / genetics
  • Huntingtin Protein / metabolism
  • Huntington Disease / genetics
  • Huntington Disease / metabolism
  • Huntington Disease / pathology*
  • Mice
  • Mice, Inbred C57BL
  • Microscopy, Confocal / instrumentation
  • Microscopy, Confocal / methods*
  • Models, Biological
  • Neural Stem Cells / metabolism
  • Neural Stem Cells / ultrastructure
  • Neurons / metabolism
  • Neurons / ultrastructure*
  • Primary Cell Culture
  • Single-Cell Analysis / instrumentation
  • Single-Cell Analysis / methods*
  • Tissue Culture Techniques


  • HTT protein, human
  • Huntingtin Protein