Segmentation and image analysis pipeline for the investigation of lineage marker expression in early human development

The pipeline makes possible the analysis of confocal imaging data acquired from preimplantation human embryos at blastocyst stage.

Through several stages, the pipeline first performs nuclear segmentation throughout the entire human blastocyst, including the inner cell mass. The map of nuclei is then used to track each nucleus, extract, and integrate quantitative information from the identified nuclei in 3D. The quantification of fluorescence intensity measurements from individual nuclei in several wavelengths enables the analysis of lineage marker expression, and quantification of signalling pathway activities.