3D Reconstructions
We are producing 3D reconstructions from serial plastic sections of zebrafish embryos and larvae (Moorman lab).
Scanning for 3D reconstructions is accomplished on a single-slide Aperio ScanScope GL. Each slide was "pre-scanned" to provide a preliminary image used to set the final focus for each section on the slide. One focus point was placed on each section in the pre-scanned image. Each focus point was then manually focused to assure that the image of each section was in focus on the final scanned imaged. Following the scan, an image of each individual section was extracted using Aperio ImageScope software and saved in jpeg format (the only image format the 3D reconstruction software accepts). Using Adobe Photoshop, the jpeg images were rotated so that the dorsal surface was at the 12 o'clock position. All images were numbered sequentially from rostral to caudal. The sequentially numbered jpeg images were then loaded into WinSurf SURFdriver software for reconstruction.
WinSurf software was used to create 3D reconstructions. The initial step of reconstruction was to outline/contour the skin in every third section (every 9 microns), then to outline/contour the individual organs. After the organs were outlined/contoured, the contours were aligned. Contours in each section were aligned to those of the preceding section. Aligning was simplified by embedding straight rat/mouse whiskers around the embryo. Initial alignment was done using contours of the hairs. Final alignment was done by "nudging" the organ contours as needed. Once all sections were aligned, each organ was assigned a specific color and the final 3D reconstruction was created.
