DOI: 10.6084/m9.figshare.11307431
title: Phmamm-U0126-1 (previously published as Astec-U0126-Pm1; U0126 treated <i>Phallusia mammillata</i> embryo, live SPIM imaging, stages 5-13)

description: <b>Phmamm-U0126-1 (previously published as Astec-U0126-Pm1)</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 <i>Phallusia mammillata</i> under pharmacological perturbation. Cell membranes were fluorescently labeled by microinjection of mRNA encoding PH-tdTomato, and ERK signaling dynamics were monitored using the ERK-KTR-mClover biosensor, both injected into an unfertilized egg. The embryo was incubated in the presence of 2 µM U0126 (MEK inhibitor) starting from early stage 5a (16-cell stage).<br><b>Imaging conditions:</b><br>The embryo was imaged with a MuVi-SPIM light-sheet microscope from the early 16-cell stage (Tp0, St. 5a) up to the late gastrula stage (Tp110, St. 13). Acquisitions were performed every 2 minutes at 17 °C in artificial seawater (ASW, salinity: 38 ppt) supplemented with 2 µM U0126 throughout the experiment.<br><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-U0126-1 was temporally aligned to it. In the normalized timeline, the acquisition of Phmamm-U0126-1 corresponds to a starting point (t0) of approximately <b>169</b><b> minutes post fertilization (tpf)</b>, with an effective acquisition interval of <b>1.86 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-U0126-1 with Phmamm-8 and the other ascidian embryo datasets.<br><b>Data processing:</b><br>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 executed using the ASCIDIAN package (documentation available here).<b>Dataset versions:</b>Guignard et al., 2020:Four-angle fusion images (ASTEC pipeline) provided in .inr format (Astec-U0126-Pm1_fuse.tar).Whole-cell segmentation images in .inr format (Astec-U0126-Pm1_post.tar).Individual cell geometric properties provided in .xml and .pkl formats (Astec-U0126-Pm1_properties.tar).Biasuz et al., 2025 (v2):Four-angle fusion images (ASTEC pipeline), temporally registered to compensate for embryo movements, provided in .nii format (Phmamm-U0126-1-v2_intrareg_fuse.tar.gz).Whole-cell segmentation images, temporally registered, provided in .nii format (Phmamm-U0126-1-v2_intrareg_post.tar.gz).Individual cell geometric and naming properties in .xml format (Phmamm-U0126-1-v2_intrareg_properties.tar.gz).For additional details about the .nii format, please refer to this resource.<br>