Mouse data for whole-embryo lineage reconstruction with linajea

This article enables access to the mouse dataset (140521) for "Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations" (Malin-Mayor et al. 2023, DOI: https://doi.org/10.1038/s41587-022-01427-7).Here we provide the ground truth tracks used to train the deep learning model, the trained networks, and the predicted tracks. Additionally, we provide information on how to access the image data, although it is not uploaded here due to size. Related artifacts include the source code for experiments and methods.Image DataThe image dataset in n5/zarr format (as used in Malin-Mayor et al. 2023) can be accessed at the following Dropbox link: https://www.dropbox.com/scl/fi/2mt7jxmtl80s3zf2byfyr/140521_mouse.tar.gz?rlkey=n5r311whn8ky4gdabybjdekcc&dl=0. This image dataset was originally published in "In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level" ( McDole et al. 2018, DOI: https://doi.org/10.1016/j.cell.2018.09.031), and can also be accessed in the Image Dataset Repository in .klb format along with associated metadata at https://idr.openmicroscopy.org/webclient/?show=project-502.Ground Truth TracksInside gt_tracks.zip there are a number of files containing different subsets of tracks. Each has the following columns separated by tabs: time, z, y, x, cell_id, parent_id, track_id.tracks.txt is the main file containg manual annotations of individual cells from start to end of video used to train the model. These tracks are sparse, but each cell included in the tracks.txt had its whole lineage traced as completely as possible from start to end of the video.division_tracks.txt is a different set of manually annotated tracks, where each track is around 5 frames long and centers around a division. daughter_cells.txt is a subset of division_tracks.txt containing only the cells directly after a division event, and was generated for convenient and efficient training of models where divisions are oversampled.full_frame_divisions.txt is a set of manually annotated division points (points right before the cell divides) that are as complete as possible for target time points 120, 240, and 360 and the adjacent time frames, which was used for evaluation and not model training.Trained Modelstrained_networks.zip includes all networks trained on the mouse dataset. The model we suggest using for best performance is described in 140521_mouse_simple_train_all_config.json and the weights are included in trai