Résumé
Phmamm-9 (previously published as Astec-Pm9)Organism: Phallusia mammillata (Phlebobranch ascidian)Description:This dataset contains live imaging data of embryonic development in Phallusia mammillata. The cell membranes were fluorescently labeled by microinjection of mRNA encoding PH-citrine into an unfertilized egg.Imaging conditions:The embryo was imaged with a MuVi-SPIM light-sheet microscope for ~2.5 hours, from the 76-cell stage (Tp1, St. 9) up to the mid gastrula stage (Tp63, St. 12). Acquisitions were performed 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. To enable direct comparison across datasets, developmental time was normalized based on cell number. Phmamm-8 was chosen as the reference embryo, and Phmamm-9 was temporally aligned to it. In the normalized timeline, the acquisition of Phmamm-9 corresponds to a starting point (t0) of approximately 260 minutes post fertilization (tpf), with an effective acquisition interval of 1.83 minutes. This temporal alignment was performed using the ASCIDIAN package (see documentation for details). This allows stage-by-stage comparison of Phmamm-9 with Phmamm-8 and the other 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-Phmamm9-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-Phmamm9-v2_post.tar.gz archive file).Individual cell geometric and naming properties are shared in .xml format (Astec-Phmamm9-v2_properties.tar.gz archive file).For additional details about the .nii format, please refer to this resource.