Division of Embryology, National Institute for Basic Biology, Okazaki, Japan.
Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan.
Dev Growth Differ. 2023 Jan;65(1):65-74. doi: 10.1111/dgd.12835. Epub 2023 Jan 14.
Three-dimensional (3D) registration (i.e., alignment) between two microscopic images is very helpful to study tissues that do not adhere to substrates, such as mouse embryos and organoids, which are often 3D rotated during imaging. However, there is no 3D registration tool easily accessible for experimental biologists. Here we developed an ImageJ-based tool which allows for 3D registration accompanied with both quantitative evaluation of the accuracy and reconstruction of 3D rotated images. In this tool, several landmarks are manually provided in two images to be aligned, and 3D rotation is computed so that the distances between the paired landmarks from the two images are minimized. By simultaneously providing multiple points (e.g., all nuclei in the regions of interest) other than the landmarks in the two images, the correspondence of each point between the two images, i.e., to which nucleus in one image a certain nucleus in another image corresponds, is quantitatively explored. Furthermore, 3D rotation is applied to one of the two images, resulting in reconstruction of 3D rotated images. We demonstrated that this tool successfully achieved 3D registration and reconstruction of images in mouse pre- and post-implantation embryos, where one image was obtained during live imaging and another image was obtained from fixed embryos after live imaging. This approach provides a versatile tool applicable for various tissues and species.
三维（3D）配准（即对齐）在研究不附着于基质的组织（如经常在成像过程中 3D 旋转的小鼠胚胎和类器官）时非常有帮助。然而，对于实验生物学家来说，没有易于使用的 3D 配准工具。在这里，我们开发了一种基于 ImageJ 的工具，它允许进行 3D 配准，并伴随对准确性的定量评估和 3D 旋转图像的重建。在这个工具中，在要对齐的两个图像中手动提供几个标记点，并计算 3D 旋转，使得来自两个图像的成对标记点之间的距离最小化。通过同时在两个图像中提供多个点（例如，感兴趣区域中的所有核）而不是标记点，可以定量探索两个图像之间每个点的对应关系，即一个图像中的某个核与另一个图像中的哪个核相对应。此外，将 3D 旋转应用于两个图像中的一个图像，从而重建 3D 旋转图像。我们证明了该工具成功地实现了小鼠植入前和植入后胚胎的 3D 配准和重建，其中一个图像是在活体成像过程中获得的，另一个图像是在活体成像后从固定胚胎中获得的。这种方法提供了一种适用于各种组织和物种的通用工具。
