Published Resources and Data
Machine learning model for 3D segmentation of cell membranes in the mouse embryo: 10.5281/zenodo.6384845
The model performs on light-sheet microcopy data.
Machine learning model for 3D segmentation of cell nuclei in the mouse embryo: 10.5281/zenodo.6383429
The model performs on confocal microscopy data.
Raw ground-truth datasets for training and validation of the 3D segmentation model: https://zenodo.org/records/6546550
Code: https://github.com/kreshuklab/mouse-embryo-seg
Raw single-cell RNA sequencing data from 4.5 days post fertilisation (d.p.f) (E4.5) and 5.25 d.p.f (E5.25) mouse embryos, dissected from the uterus, and day two (D2) and day three (D3) mouse embryos, grown in 3E-uterus.
Source publication:
Bondarenko V, Nikolaev M, Kromm D, Belousov R, Wolny A, Blotenburg M, Zeller P, Rezakhani S, Hugger J, Uhlmann V, Hufnagel L, Kreshuk A, Ellenberg J, van Oudenaarden A, Erzberger A, Lutolf MP, Hiiragi T (2023). Embryo-uterine interaction coordinates mouse embryogenesis during implantation. EMBO J; 42 (issue 17): e113280.
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