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