Membrane staining and segmentation of a developing mouse embryo from 4 to 26 cells

<h1>Intent</h1> <p>The role of this dataset is to provide an example of segmentable and trackable data using signal from cell membrane. This dataset contains one file with the pre-processed imaged embryo (imaging.zip -&gt; imaging.tif) and one file with the outcome of a segmentation using Cellpose (segmentation.zip -&gt; segmentation.tif).</p> <blockquote> <p>This embryo corresponds to the embryo "C1" in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a></p> </blockquote> <h1>Animal</h1> <p>This set of data represents a mouse embryo developing from the 4-cell stage. The embryo at the last processed timepoint has 26 cells.&nbsp;The mother and the father were both mTmG animals (tdTomato anchored at the membrane of the cells).</p> <blockquote> <p>Details can be found in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a></p> </blockquote> <h1>Culture conditions</h1> <p>The embryo was imaged in an inverted SPIM from Luxendo (now Bruker), laying at the bottom of a PFE imaging dish. The embryo developed in a small pocket made by deforming the PFE with a glass tip. We used approx. 150&mu;L of KSOM-AA to cutlure the embryos at 37&ordm;C &plusmn; 0.2&ordm;C in 5% CO2 and 5% O2. The medium was covered with approx. 100&mu;L of mineral oil.</p> <blockquote> <p>Details can be found in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a></p> </blockquote> <h1>Imaging conditions</h1> <p>The tdTomato was excited with a 561nm laser using as little intensity as possible (0% in the settings + a small fraction leaking through the shutter). We used a 561 LP filter to acquire the signal. Imaging was set with a lateral resolution of 0.208&mu;m and a axial resolution of 1&mu;m. Because of technical issues with the stage of the microscope at the time, the resulting axial resolution was ultimately 1.338&mu;m. In total, 181 slices were acquired per time point. Two consecutive timepoints start with 15 minutes of interval.</p> <p>Although this embryo was imaged for a longer period of time, this dataset shows only the first 117 timepoints.</p> <blockquote> <p>Details can be found in the <a href="https://doi.org/10.1126/science.adh1145" target="_blank" rel="noopener">original publication</a></p> </blockquote> <h1>Processing conditions</h1> <table> <tbody> <tr> <td><strong>Operation</strong></td> <td><strong>Lateral resolution</strong></td> <td><strong>Axial resolution</strong></td> <td><strong>File</strong></td> </tr> <tr> <td><strong>Imaging</strong></td> <td>0.208 &mu;m</td> <td>1.338 &mu;m</td> <td>-</td> </tr> <tr> <td><strong>Cropping<br></strong></td> <td>0.208 &mu;m</td> <td>1.338 &mu;m</td> <td>-</td> </tr> <tr> <td><strong>Lateral binning (average)</strong></td> <td>0.416 &mu;m</td> <td>1.338 &mu;m</td> <td>-</td> </tr> <tr> <td><strong>Isotropic rescaling</strong></td> <td>0.416 &mu;m</td> <td>0.416 &mu;m</td> <td>-</td> </tr> <tr> <td><strong>Lateral binning (average)</strong></td> <td>0.832 &mu;m</td> <td>0.832 &mu;m</td> <td>imaging.tif</td> </tr> <tr> <td><strong>Segmentation (cellpose)</strong></td> <td>0.832 &mu;m</td> <td>0.832 &mu;m</td> <td>segmentation.tif</td> </tr> </tbody> </table>