Cellular 3D-reconstruction and analysis in the human cerebral cortex using automatic serial sections

Research output: Contribution to journalJournal articleResearchpeer-review

  • Nick Y. Larsen
  • Xixia Li
  • Xueke Tan
  • Gang Ji
  • Jing Lin
  • Grazyna Rajkowska
  • Jesper Møller
  • Ninna Vihrs
  • Sporring, Jon
  • Fei Sun
  • Jens R. Nyengaard

Techniques involving three-dimensional (3D) tissue structure reconstruction and analysis provide a better understanding of changes in molecules and function. We have developed AutoCUTS-LM, an automated system that allows the latest advances in 3D tissue reconstruction and cellular analysis developments using light microscopy on various tissues, including archived tissue. The workflow in this paper involved advanced tissue sampling methods of the human cerebral cortex, an automated serial section collection system, digital tissue library, cell detection using convolution neural network, 3D cell reconstruction, and advanced analysis. Our results demonstrated the detailed structure of pyramidal cells (number, volume, diameter, sphericity and orientation) and their 3D spatial organization are arranged in a columnar structure. The pipeline of these combined techniques provides a detailed analysis of tissues and cells in biology and pathology.

Original languageEnglish
Article number1030
JournalCommunications Biology
Volume4
Issue number1
Number of pages15
ISSN2399-3642
DOIs
Publication statusPublished - Dec 2021

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