Résumé
Phmamm-8 (previously published as Astec-Pm8)Organism: Phallusia mammillata (Phlebobranch ascidian).Description: This dataset contains live imaging data of embryonic development in Phallusia mammillata. Cell membranes were fluorescently labeled by microinjection of mRNA encoding PH-citrine into unfertilized eggs.Imaging conditions:The embryo has been live imaged with a MuVi-SPIM light-sheet microscope from the 64-cell stage (Tp 1, St. 8, 4hpf) up to the early neurula (Tp 88, St. 14) every 2 minutes at 18°C in artificial seawater (ASW, salinity: 38 ppt). Temporal alignment:Embryonic development in Phallusia mammillata shows natural variability in timing between individuals, even under similar conditions. To enable direct comparison across datasets, developmental time was normalized based on cell number. Among the available acquisitions, Phmamm-8 was chosen as the reference embryo, and its timeline was used to align other embryos by rescaling their time post-fertilization (tpf) and acquisition intervals. Phmamm-8 thus serves as the temporal reference for the entire collection of ascidian embryo datasets.Data processing:Fusion of images from four angles, whole-cell segmentation and temporal registration to correct for embryo movement were performed using the ASTEC pipeline (detailed documentation available here).In version 2, cell identification and fate assignments were further refined using the ASCIDIAN package (documentation available here).Dataset versions:Guignard et al, 2020:The four angle fusion images obtained using the ASTEC pipeline are shared in .inr format (fuse.tar.gz archive file).Whole cells were segmented using the ASTEC pipeline and shared in .inr format (post.tar.gz archive file).Surface meshes (.obj) povided in the mesh.tar.gz archive were produced using the VTK library and MeshLab.Individual cell geometric properties are shared in two different formats, .xml and .pkl (properties.tar.gz archive file).Biasuz et al, 2025 (v2):The four angle fusion images obtained using the ASTEC pipeline and temporally registered to compensate for embryo movements in the microscope are shared in .nii format (Astec-Phmamm8-v2_fuse.tar.gz archive file).Whole cells were segmented using the ASTEC pipeline and temporally registered to compensate for embryo movements in the microscope are shared in .nii format (Astec-Phmamm8-v2_post.tar.gz archive file).Individual cell geometric and naming properties are shared in .xml format (Astec-Phmamm8-v2_properties.tar.gz archive file).For additional details about the .nii format, please refer to this resource.