Videos of Embryonic Wound Healing in Drosophila and Wound Segmentation

<p>We collect a dataset of time-lapse sequences of <em>Drosophila</em>&nbsp;embryos healing after a laser-induced wound. Altogether we acquire 61 sequences, which we split into train, validation, and test sets of 44, 12, and 5 sequences, respectively.&nbsp;<br> We use embryos expressing a GFP tagged myosin II (sqhGFP) imaged at stage 17. The embryos are collected after aging for 16&nbsp;hours at 18&deg;C. They are mounted on a coverslip covered with heptane glue for conventional confocal microscopy and<br> by mineral oil to prevent drying. Laser ablation is performed with a pulsed laser. The time-lapse sequences are acquired <em>in vivo&nbsp;</em>using an Olympus IXplore SpinSR10 at room temperature. The samples are illuminated by laser with <span>\(488\,\textrm{nm} \)</span>&nbsp;wavelength using a&nbsp;<span>\(60\, \times \, 1.42 \)</span>&nbsp;NA oil immersion objective.</p> <p>The individual frames are taken once every minute. Each sequence captures the entire closure of the wound, resulting in an average length of 120 frames. Each frame has&nbsp;<span>\(1152\times1152\)</span>&nbsp;pixels and captures the whole embryo with <span>\(4.6\, \mu \textrm{m/pixel}\)</span>&nbsp;image resolution. A z-stack of the embryo is imaged at each time step with a z-step size of <span>\(1\, \mu \textrm{m}\)</span>.&nbsp;<br> The time-resolved z-stacks are max-projected along the z-axis, and registered by SIFT algorithm in Fiji. The wounds are segmented by a custom stable U-Net-like architecture and manually refined in napari. As each frame includes the entire embryo, it is cropped to a region of <span>\(256\times 256\)</span>&nbsp;pixels containing the wound and downsampled to <span>\(128\times 128\)</span>&nbsp;by bicubic interpolation.<br> <br> The processed timelapse sequences are in the folder Video of the Dataset.zip, and their skeletonized segmentations in the folder Segmentations.&nbsp;</p>