EMERGE: An interactive online database of quantitative morphological dynamics during Caenorhabditis elegans embryonic development with resolved cell lineage

1. Data.zip — The full EMERGE csv dataset, matching the content available for download at emergedb.com/download. It includes the segmented 3D cell morphology models with their 12 quantitative morphology features per cell, and gene expression data from fluorescence reporter and scRNA-sequencing. 2. Figure.zip — Source code used to generate the figures, including Figure 1, Figure 2, and the Graphical Abstract. 3. Data_processing.zip — The complete data-processing pipeline scripts, covering every step from raw output through segmentation and gene expression quantification, to the final relational database-format tables. 4. EMERGE.ipynb — A self-contained interactive Jupyter notebook for fetching, visualizing, and analyzing EMERGE data in Python. 5. Web platform source code — The EMERGE interactive web application is hosted separately on GitHub at https://github.com/PikaPatch/EMERGE. 6. Image data and related morphology resources — Image datasets are available through the Google Drive folder, accompanied by cell-morphology datasets, visualization tools, and web platforms spanning multiple C. elegans embryogenesis studies. CShaper dataCell-morphology data from 17 compressed C. elegans embryos, captured at approximately 1.5-minute intervals from early development to the ~350-cell stage. Dataset G: Cell-labeled data Dataset H: Fate-labeled data Associated tool: ITK-SNAP-CVE, for automatic visualization and analysis of cell-morphology data Reference: Cao J†, Guan G†, Ho VWS†, Wong MK, Chan LY, Tang C*, Zhao Z*, Yan H*. Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation. Nature Communications (2020). CMap dataCell-morphology data from eight uncompressed C. elegans embryos, recorded at approximately 1.5-minute intervals through the ~550-cell stage. Dataset C: Cell-labeled data before filtering Dataset D: Fate-labeled data before filtering Dataset E: Cell-labeled data after filtering Dataset F: Fate-labeled data after filtering Associated platform: CMOS, an online platform for visualizing and analyzing cell-morphology data together with gene-expression data Reference: Guan G†, Li Z†, Ma Y†, Ye P†, Cao J, Wong MK, Ho VWS, Chan LY, Yan H*, Tang C*, Zhao Z*. Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry. Nature Communications (2025). EmbSAM dataCell-morphology data from four compressed embryos and two uncompressed embryos, acquired every 10 seconds through the ~20-cell stage. Associated tools and platforms: ITK-SNAP-CVE for automated visualization and analysis; CMOS/EmbSAM for online visualization and analysis of morphology data at 10-second temporal resolution Reference: Guan G†, Zhao C†, Li Z†, Zhang P, Chen Y, Ye P, Wong MK, Chan LY, Yan H, Tang C, Zhao Z. EmbSAM: Cell boundary localization and Segment Anything Model for fast images of developing embryos. Communications Biology, under review (2025).