Realistic 3D computer model of the gerbil middle ear, featuring accurate morphology of bone and soft tissue structures

In order to improve realism in middle ear (ME) finite element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (\mu CT) recordings have been used as geometric input data for FEM models of the ME ossicles. Previously, attempts were made to obtain this data on ME soft tissue structures as well. However, due to low X-ray absorption of soft tissue, quality of these images is limited. Another popular approach is using histological sections as data for 3D models, delivering high in-plane resolution for the sections, but the technique is destructive in nature and registration of the sections is difficult. We combine data from high-resolution \mu CT recordings with data from high-resolution orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS), both obtained on the same gerbil specimen. State-of-the-art \mu CT delivers high-resolution data on the three-dimensional shape of ossicles and other ME bony structures, while the OPFOS setup generates data of unprecedented quality both on bone and soft tissue ME structures. Each of these techniques is tomographic and non-destructive, and delivers sets of automatically aligned virtual sections. The datasets coming from different techniques need to be registered with respect to each other. By combining both datasets, we obtain a complete high-resolution morphological model of all functional components in the gerbil ME. The resulting three-dimensional model can be readily imported in FEM software and is made freely available to the research community. In this paper, we discuss the methods used, present the resulting merged model and discuss morphological properties of the soft tissue structures, such as muscles and ligaments.

💡 Research Summary

The paper presents a comprehensive workflow for constructing a high‑resolution three‑dimensional model of the gerbil middle ear (ME) that includes both bony and soft‑tissue structures. Traditional finite‑element models have relied on low‑resolution or manually drawn geometries, especially for ligaments, tendons, and muscles, limiting biomechanical accuracy. To overcome this, the authors combined two complementary, non‑destructive imaging modalities. First, micro‑scale X‑ray computed tomography (µCT) was used to capture the ossicles, bony labyrinth, and tympanic membrane at an isotropic voxel size of 8.5 µm, providing excellent contrast for mineralized tissue. Because soft tissue is poorly visualized by X‑rays, orthogonal‑plane fluorescence optical‑sectioning microscopy (OPFOS) was employed after extensive specimen preparation (blood removal, formalin fixation, EDTA decalcification, graded ethanol dehydration, Spalteholz clearing, and Rhodamine B staining). OPFOS produces optical sections by intersecting a thin laser sheet with the transparent specimen, yielding simultaneous high‑resolution images of bone and soft tissue.

The authors manually segmented thousands of slices using Amira software, preferring expert‑driven delineation over automated thresholding. Marching‑cubes triangulation generated surface meshes for each structure. µCT data served as the reference coordinate system; bone fragments present in the OPFOS stacks were used to compute rigid transformations that aligned the OPFOS soft‑tissue meshes with the µCT model. After merging, a complete ME model comprising the tympanic membrane, malleus, incus, stapes, the surrounding ligaments, and the two middle‑ear muscles was obtained. The final meshes are provided in STL format for free download, enabling direct import into FEM packages such as ANSYS or COMSOL.

The study also discusses methodological limitations. OPFOS requires full transparency, which can cause tissue shrinkage and deformation, especially of the extremely thin tympanic membrane; therefore the membrane geometry was retained from the µCT scan. Stripe artifacts from uneven illumination were mitigated by dual‑sheet illumination. Only one specimen was processed for OPFOS, while three were scanned with µCT, highlighting the need for larger sample sizes to assess biological variability.

Overall, the work delivers a validated, high‑fidelity 3D dataset that can serve as a benchmark for middle‑ear biomechanics, improve the realism of FEM simulations, and support the design of auditory prostheses or educational tools.