E18.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain Atlas

3D imaging necessitates corresponding 3D anatomical atlases, but generating such atlases is time consuming and challenging. Substantial efforts have generated such atlases including the Allen Developing Mouse Brain Atlas (ADMBA) but are typically limited by the process of serial 2D annotation for 3D reconstruction leading to artifacts. We have developed an automated, edge-aware atlas refinement method to curate existing atlases in a topologically consistent, 3D manner. Applying this approach to the E18.5 atlas in the ADMBA, we inferred labels for incompletely labeled areas, smoothed the labels in 3D, and realigned the labels to the underlying anatomical edges. As required, we also rotated images in 3D for midline symmetry and resized a stretch of compressed sagittal label planes.

三维成像需要配套的三维解剖图谱（anatomical atlases），但构建此类图谱既耗时又极具挑战。已有大量研究工作生成了包括艾伦发育小鼠脑图谱（Allen Developing Mouse Brain Atlas，ADMBA）在内的相关图谱，但这类方法通常受限于用于三维重建的连续二维标注流程，易产生伪影（artifacts）。我们开发了一种自动化、边缘感知（edge-aware）的图谱优化方法，能够以拓扑一致（topologically consistent）的三维方式对现有图谱进行整理校正。将该方法应用于ADMBA中的E18.5图谱时，我们对未完全标注的区域推断出了标注标签，在三维空间中对标签进行平滑处理，并将标签重新对齐至对应的解剖学边缘。此外，我们还按照需求对三维图像进行旋转以实现中线对称，并调整了一段受压变形的矢状位（sagittal）标注平面的尺寸。