3D time-lapse microscopy paired with endpoint lineage analysis in mouse blastocysts

Michael J. Pokrass, Sergi Regot

Research output: Contribution to journalArticlepeer-review


Determining how signaling dynamics relate to gene expression and cell fate is essential to understanding multicellular development. We present a unified live imaging and lineage analysis method that allows integrated analysis of both techniques in the same mouse embryos. This protocol describes the embryo isolation, confocal imaging, immunofluorescence, and in silico alignment required to connect time-lapse and endpoint measurements. By utilizing different biosensors and fixed readouts, this method allows interrogation of signaling dynamics that specify cell fates in developing embryos. For complete details on the use and execution of this protocol, please refer to Pokrass et al. (2020).

Original languageEnglish (US)
Article number100446
JournalSTAR Protocols
Issue number2
StatePublished - Jun 18 2021


  • Cell differentiation
  • Microscopy
  • Signal transduction
  • Single cell

ASJC Scopus subject areas

  • General Medicine
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology
  • General Neuroscience


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