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To determine the three-dimensional (3-D) shape of a live embryo is a technically challenging task. The authors show that reconstructions of live embryos can be done by collecting images from different viewing angles using a robotic macroscope, establishing point correspondences between these views by block matching, and using a new 3-D reconstruction algorithm that accommodates camera positioning errors. The algorithm assumes that the images are orthographic projections of the object and that the camera scaling factors are known. Point positions and camera errors are found simultaneously. Reconstructions of test objects and embryos show that meaningful reconstructions are possible only when camera positioning and alignment errors are accommodated since these errors can be substantial. Reconstructions of early-stage axolotl embryos were made from sets of 33 images. In a typical reconstruction, 781 points, each visible in at least three different views, were used to form 1511 triangles to represent the embryo surface. The resulting reconstruction had a mean radius of error of 0.27 pixels (1.1 μm). Mathematical properties of the reconstruction algorithm are identified and discussed.