Dataset supporting "Nuclear instance segmentation and tracking for preimplantation mouse embryos"

For investigations into fate specification and morphogenesis in time-lapse images of preimplantation embryos, automated 3D instance segmentation of nuclei is invaluable. Supervised machine learning approaches can radically improve segmentation accuracy, but they often require large amounts of annotated 3D data. Using selective plane illumination microscopy (SPIM) we acquired 3D live images of H2B-miRFP720-expressing preimplantation embryos at various developmental stages and created a new ground-truth dataset with full 3D nuclear instance segmentation. This dataset, which we call BlastoSPIM (concatenation of blastocyst and SPIM), is one of the largest and most complete of its kind and can be used for benchmarking different segmentation methods. BlastoSPIM is split into two parts: 1.0, mostly containing images of early embryos, and 2.0, containing images of late blastocysts. The BlastoSPIM 1.0 dataset includes 573 fully annotated 3D images of nuclei in mouse embryos; across all images, there are 11708 individual nuclear instances annotated and 116 annotated polar bodies. The BlastoSPIM 2.0 dataset consists of 80 annotated images of late-stage embryos with a total of 6628 nuclear instances. The quality, detail, and size of the BlastoSPIM dataset makes it unique relative to other publicly available ground truth datasets for nuclear instance segmentation. See blastospim.flatironinstitute.org for more details and models trained on this dataset.

Funding: Research reported in this publication was supported by the National Institutes of Health under award numbers R01HD110577 (E.P.) and R01HD107026 (E.P.) and the National Center for Advancing Translational Sciences (NCATS), a component of the National Institutes of Health (NIH) under award number TL1TR003019 (fellowship, R.P.K.-Y.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The computations in this work were performed at facilities supported by the Scientific Computing Core at the Flatiron Institute, a division of the Simons Foundation.