DOI: 10.6084/m9.figshare.11307293
title: Phmamm-U0126-2 (previously published as Astec-U0126-Pm2; U0126 treated

description: <b>Phmamm-U0126-2 (previously published as Astec-U0126-Pm2)</b><br><b>Organism: </b><i>Phallusia mammillata</i> (Phlebobranch ascidian)<b>Condition</b>: Perturbation with MEK inhibitor U0126<b>Description:</b><br>This dataset contains live imaging data of embryonic development in Phallusia mammillata under pharmacological perturbation. The cell membranes were fluorescently labeled by microinjection of mRNA encoding PH-tdTomato and ERK-KTR-mClover into an unfertilized egg. In addition, mRNA encoding ERK-KTR-mClover was co-injected as a biosensor of ERK activity. The embryo was incubated in the presence of 6 µM U0126 (MEK inhibitor) starting from the 16-cell stage (St. 5).<br><b>Imaging conditions:</b><br>The embryo was imaged with a MuVi-SPIM light-sheet microscope from the early 44-cell stage (Tp30, St. 7) up to the early gastrula stage (Tp79, St. 11). Acquisitions were performed every 2 minutes at 17 °C in artificial seawater (ASW, salinity: 38 ppt) supplemented with 6 µM U0126 throughout the experiment.<br><b>Temporal alignment:</b><br>Embryonic development in <i>Phallusia mammillata</i> shows natural variability in timing between individuals. To enable direct comparison across datasets, developmental time was normalized based on cell number evolution in the epidermis. Indeed, epidermal territories retain their normal identities and division patterns despite MEK inhibition using U0126, providing a reliable temporal reference. <b>Phmamm-8 was chosen as the reference embryo</b>, and Phmamm-U0126-2 was temporally aligned to it. In the normalized timeline, the acquisition of Phmamm-U0126-2 corresponds to a starting point (t0) of approximately <b>178</b><b> minutes post fertilization (tpf)</b>, with an effective acquisition interval of <b>1.66 minutes</b>. This temporal alignment was performed using the <b>ASCIDIAN package</b> (see documentation for details). This allows stage-by-stage comparison of Phmamm-U0126-2 with Phmamm-8 and the other ascidian embryo datasets.<br><b>Data processing:</b>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). Version 3 was re-segmented over a longer developmental window (Tp30–79 for v3 versus Tp30–50 for v1) and with a more recent release of ASTEC compared to version 1.In version 3 : cell identification and fate assignments were executed using the ASCIDIAN package (documentation available here).<b>Dataset versions:</b>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 (v3):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 (Phmamm-U0126-2-v3_intrareg_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 (Phmamm-U0126-2-v3_intrareg_post.tar.gz archive file).Individual cell geometric properties are shared in .xml format (Phmamm-U0126-2-v3_properties.tar.gz archive file).For additional details about the .nii format, please refer to this resource.<br>