![]() ![]() ![]() 1a), for which each object is registered to every other. We have developed an accessible and generally applicable, software toolkit to achieve efficient landmark-free group-wise registration of corresponding objects segmented from 3D imaging datasets, such that objects converge towards their consensus morphology.Īn efficient method for 3D group-wise elastic registration without landmarksĪtlas Toolkit ( Supplementary Software 1) is a collection of Fiji/ImageJ plugins 6 developed to achieve group-wise elastic registration of 3D (XYZ) objects by decomposing the alignment problem into a sequence of orthogonal 2D elastic registrations (e.g. Moreover, an over-reliance on molecular markers will also consume precious data channels, limiting the information that may be captured per specimen. Unfortunately, datasets from isolated tissues and organ primordia such as the developing eye offer few or no well-defined landmarks, making the placement of fiduciary markers impossible. to reveal neuropil morphology in brain specimens 5. In other cases, landmarks may be identified by molecular labelling, e.g. For landmark-rich objects such as whole embryos, user-defined fiduciary markers identifying corresponding features may be employed to guide the process 3, 4. Registration is often performed in pair-wise fashion 3, 4, with multiple images being registered to a pre-selected reference specimen. Image registration provides a means of mapping diverse observations from independent embryo specimens into a unified coordinate system, thereby permitting system-level analysis. There is a need therefore to develop broadly applicable tools for integrating three- and four-dimensional (3D & 4D) imaging datasets from multiple specimens 2. Typically in fluorescence microscopy studies, it is possible to observe a maximum of three or four molecular species in a single embryo specimen, depending on the availability of orthogonal fluorescent probes. Imaging combined with computational analysis is an important tool for illuminating organogenesis in the embryo 1. ![]()
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