Large-scale time-lapse microscopy of Oct4 expression in human embryonic stem cell colonies

Stem Cell Res. 2016 Jul;17(1):122-9. doi: 10.1016/j.scr.2016.05.012. Epub 2016 May 22.


Identification and quantification of the characteristics of stem cell preparations is critical for understanding stem cell biology and for the development and manufacturing of stem cell based therapies. We have developed image analysis and visualization software that allows effective use of time-lapse microscopy to provide spatial and dynamic information from large numbers of human embryonic stem cell colonies. To achieve statistically relevant sampling, we examined >680 colonies from 3 different preparations of cells over 5days each, generating a total experimental dataset of 0.9 terabyte (TB). The 0.5 Giga-pixel images at each time point were represented by multi-resolution pyramids and visualized using the Deep Zoom Javascript library extended to support viewing Giga-pixel images over time and extracting data on individual colonies. We present a methodology that enables quantification of variations in nominally-identical preparations and between colonies, correlation of colony characteristics with Oct4 expression, and identification of rare events.

Keywords: Cell therapy; Fluorescence microscopy; Live cell imaging; Pluripotency; Stem cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Human Embryonic Stem Cells / cytology*
  • Human Embryonic Stem Cells / metabolism
  • Humans
  • Image Processing, Computer-Assisted*
  • Microscopy, Fluorescence*
  • Octamer Transcription Factor-3 / metabolism*
  • Software
  • Time-Lapse Imaging*


  • Octamer Transcription Factor-3
  • POU5F1 protein, human