Internal Versus External Neighbourhood – user-friendly, open-source software for analysing embryo cell positions in 3D
The landing matters when it comes to embryo development. After a fertilised egg travels through the fallopian tubes it needs to land, then implant, into the womb. In preparation, its cells shrink and architecture changes. Researchers investigate the mechanics of this process using novel software called IVEN, Internal Versus External Neighbourhood. IVEN classifies cells into different groups based on their position and counts the number of neighbours they have in 3D. IVEN was applied to fluorescence microscopy images (pictured, cell nuclei in pink) of mouse embryos grown in dishes and analysed at different stages (left to right). To test the effectiveness of IVEN, the team added the chemical FGF-4, which is known to flatten and disperse cells in an embryo. The software confirmed these effects but also showed that adding FGF-4 changed overall embryo architecture. And it revealed that cells only start growing on implantation. IVEN can therefore help uncover early embryo mechanics.
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