Cossellu Daniele, Vivado Elisa, Batti Laura, Gantar Ivana, Pizzala Roberto, Perin Paola
Department of Molecular Medicine, University of Pavia, Pavia, Italy.
Wyss Center for Bio and Neuro Engineering, Geneva, Switzerland.
PeerJ. 2025 May 26;13:e19512. doi: 10.7717/peerj.19512. eCollection 2025.
Volumetric atlases are an invaluable tool in neuroscience and otolaryngology, greatly aiding experiment planning and surgical interventions, as well as the interpretation of experimental and clinical data. The rat is a major animal model for hearing and balance studies, and a detailed volumetric atlas for the rat central auditory system (Waxholm) is available. However, the Waxholm rat atlas only contains a low-resolution inner ear featuring five structures. In the present work, we segmented and annotated 34 structures in the rat inner ear, yielding a detailed volumetric inner ear atlas which can be integrated with the Waxholm rat brain atlas.
We performed iodine-enhanced microCT and iDISCO+-based clearing and fluorescence lightsheet microscopy imaging on a sample of rat temporal bones. Image stacks were segmented in a semiautomated way, and 34 inner ear volumes were reconstructed from five samples. Using geometrical morphometry, high-resolution segmentations obtained from lightsheet and microCT stacks were registered into the coordinate system of the Waxholm rat atlas.
Cleared sample autofluorescence was used for the reconstruction of most inner ear structures, including fluid-filled compartments, nerves and sensory epithelia, blood vessels, and connective tissue structures. Image resolution allowed reconstruction of thin ducts (reuniting, saccular and endolymphatic), and the utriculoendolymphatic valve. The vestibulocochlear artery coursing through bone was found to be associated to the reuniting duct, and to be visible both in cleared and microCT samples, thus allowing to infer duct location from microCT scans. Cleared labyrinths showed minimal shape distortions, as shown by alignment with microCT and Waxholm labyrinths. However, membranous labyrinths could display variable collapse of the superior division, especially the roof of canal ampullae, whereas the inferior division (saccule and cochlea) was well preserved, with the exception of Reissner's membrane that could display ruptures in the second cochlear turn. As an example of atlas use, the volumes reconstructed from segmentations were used to separate macrophage populations from the spiral ganglion, auditory neuron dendrites, and Organ of Corti.
We have reconstructed 34 structures from the rat temporal bone, which are available as both image stacks and printable 3D objects in a shared repository for download. These can be used for teaching, localizing cells or other features within the ear, modeling auditory and vestibular sensory physiology and training of automated segmentation machine learning tools.
体积图谱在神经科学和耳鼻喉科学中是一种非常有价值的工具，极大地有助于实验规划、手术干预以及实验和临床数据的解读。大鼠是听力和平衡研究的主要动物模型，并且有一个详细的大鼠中枢听觉系统体积图谱（瓦克斯霍尔姆图谱）。然而，瓦克斯霍尔姆大鼠图谱仅包含一个低分辨率的内耳，其具有五个结构。在本研究中，我们对大鼠内耳中的34个结构进行了分割和注释，生成了一个详细的内耳体积图谱，该图谱可与瓦克斯霍尔姆大鼠脑图谱整合。
我们对大鼠颞骨样本进行了碘增强微型计算机断层扫描（microCT）以及基于免疫标记和成像系统（iDISCO +）的清除和荧光光片显微镜成像。图像堆栈以半自动方式进行分割，并从五个样本中重建了34个内耳体积。使用几何形态测量法，将从光片和microCT堆栈获得的高分辨率分割结果注册到瓦克斯霍尔姆大鼠图谱坐标系中。
清除后的样本自发荧光用于重建大多数内耳结构，包括充满液体的腔室、神经和感觉上皮、血管以及结缔组织结构。图像分辨率允许重建细管（联合管、球囊管和内淋巴管）以及椭圆球囊管瓣膜。发现穿过骨的前庭蜗动脉与联合管相关，并且在清除后的样本和microCT样本中均可见，从而允许从microCT扫描推断管道位置。清除后的迷路显示出最小的形状变形，这通过与microCT和瓦克斯霍尔姆迷路对齐得以证明。然而，膜迷路的上半部分可能会出现不同程度的塌陷，特别是壶腹嵴顶，而下半部分（球囊和耳蜗）保存良好，但第二蜗转中的Reissner膜可能会出现破裂。作为图谱应用的一个例子，从分割中重建的体积被用于从螺旋神经节、听觉神经元树突和柯蒂器中分离巨噬细胞群体。
我们从大鼠颞骨中重建了34个结构，这些结构以图像堆栈和可打印3D对象的形式在一个共享存储库中供下载。这些可用于教学、在耳内定位细胞或其他特征、模拟听觉和前庭感觉生理学以及训练自动分割机器学习工具。
