Ankle Anatomy Netter

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Latrina Mosely

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Aug 3, 2024, 5:52:23 PM8/3/24

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Models and simulations of human function impact medicine and medical technology. Particularly, musculoskeletal modeling provides an avenue for insight into the human body, which might not be otherwise possible. However, reaching the ultimate goal of functional multi-scale human models has been slowed by the lack of freely available datasets of anatomical models and geometries. Moreover, female-specific geometries have been neglected with a widespread emphasis on male geometry. To help realize this goal, we have developed and shared complete three-dimensional musculoskeletal geometries extracted from the National Libraries of Medicine Visible Human Female and Male cryosections. Muscle, bone, cartilage, ligament, and fat from the pelvis to the ankle were digitized and exported. These geometries provide a foundation for continued work in human musculoskeletal simulation with high-fidelity deformable tissues that enable a better understanding of normal function and the evaluation of pathologies and treatments. This work is novel as it includes both the male and female Visible Human specimens, outputs at multiple levels of post-processing for maximum data reuse, and is publicly available.

Musculoskeletal modeling provides an avenue to gain insight into the human body, which might not be possible otherwise. Models and simulations of human function have had a substantial impact on medicine, medical technology, product development, and education. To highlight some of the many examples, models and simulations have been used to understand tissue pathology and treatment1,2, analyse response to impact and car-crashes3, develop and test products4, create education materials5, and build models for entertainment6. Unfortunately, the three-dimensional (3D) geometries of the human tissues used to create useful applications are infrequently offered to the public, or may be in a raw form with limited utility7. As a result, new applications must start from the beginning with the effortful and time-consuming first step in the process of building 3D tissue geometries. 3D geometries are frequently built from the segmentation of anatomy from cross-sectional images (e.g. from MRI or CT). Although geometries created from the Visible Human Project8,9 have been used in numerous research and commercial applications, they are also seldom shared. The few exceptions are example models purpose-built for applications such as car-crash analysis or electromagnetic analysis, focusing on organs and general structures for appendages7,10. Groups of tissue geometries were combined to create these models, whereas simulation of musculoskeletal movement requires detailed representation of individual muscle geometries. Furthermore, freely available muscle geometries such as those in OpenSim11 are represented by two-dimensional lines of action and frequently contain a collection of muscle representations from various specimens. Moreover, there has been widespread utilization of tissue geometries constructed from the Visible Human Male imaging dataset, mostly neglecting the availability of the Visible Human Female imaging dataset. Our work aimed to produce and publicly share a comprehensive set of individual 3D musculoskeletal geometries of the lower extremities, including both the Visible Human Female and Male, and provide the results in multiple levels of post-processing for maximum data reuse. An inherent consequence of creating 3D geometries from imaging is that raw and smoothed geometries may have some overclosure or overlap12. A novel part of this work is that the provided final geometries include no overlap and sufficient smoothing to provide a ready foundation for use in computer modeling and simulation, while staying true to the original source imaging. These geometries provide a starting point for continued work in human musculoskeletal simulation with high-fidelity deformable tissues that may enable a better understanding of normal function and the evaluation of pathologies and treatments.

The cryosection and CT images were downloaded from the National Library of Medicine ( _human.html), reduced in size for manageability, and imported into software used for segmenting geometries from medical images (ScanIP v. S-2021.06, Simpleware, Synopsys, Mountain View, CA). Image volumes were cropped to the sternum. Offsets were created using original Cartesian coordinates of images from the original dataset, and manual/automatic alignment registration in non-aligning areas.

Segmenting entailed manually selecting geometries in images using ScanIP. The researchers performing the segmentation referenced multiple anatomical sources, primarily Netter14 and Fleckenstein et al.15, and anatomical imaging applications at Radiopedia (www.radiopaedia.org) and AnatomyLearning (www.anatomylearning.com). Primal Pictures (Informa UK Limited, London) software was used as a reference for the Visible Human Male. Segmentation masks from Step 2 were exported from ScanIP as metaimage header (MHD) files to enable alteration or refinement of our digitization process by subsequent users. MHD files were included as the primary files containing the raw segmentation for use with most other commercial software, such as Mimics (Materialise, Belgium), ScanIP, and Amira (ThermoFisher Scientific, Waltham, MA).

MHD files were combined in 3D Slicer (v. 4.11.20210226, www.slicer.org) to create nearly raw raster data (NRRD) files, the standard files used in 3D Slicer for segmentation16. 3D slicer is a freely available software for reconstruction of three-dimensional geometry from medical imaging. NRRD files were included to allow for end users to quickly use 3DSlicer to view and edit segmentation in a freely available environment. NRRD masks were converted to TIFF stacks and binary labelmaps in .mat format for use in MATLAB (v. 2020b, Mathworks, Natick, MA). Muscle, bone, cartilage, ligament, and fat from the pelvis to the ankle were digitized and exported from ScanIP as raw 3D stereolithography (STL) objects without any post-processing. These raw 3D geometries may be used by others who wish to apply alternative means of post-processing than that described in steps 4 and 5.

The data and metadata describing the datasets can be found at Digital Commons @ DU:13 In total 260 geometries from the Visible Human Male and Female were extracted (Fig. 1)13. The skeletal components consist of the pelvis through the feet (Table 1); the ligament and cartilage components consist of hip, knee, and ankle cartilages and knee ligaments (Table 2); muscle components consist of 76 separate muscles from the Iliacus proximally to the Flexor Digitorum distally (Table 3), and two fat components consisting of the intramuscular fat and fascia, and the outer fat, dermis, and epidermis (Table 4).

Aligned Cryosection Images: moving proximal to distal in the Visible Human sequences of cryosection images, there are offsets in the transverse plane that require correction before beginning segmentation. The Visible Human Female images contain some challenging offsets. As correction is a time-consuming process, we have made the corrected images available for download. The corrected scans are available in DICOM, TIFF, .mat, and MHD file formats.

Aligned and Rescaled CT Images: the Visible Human CT images are useful for segmentation of tissues that are not as clear in the cryosection images. However, the original CT images are not precisely aligned with the cryosection images. We have made available the CT images aligned to the cryosection images also with offsets corrected. CT scans are full scans going from the head-to-toes. The corrected scans are available in DICOM, TIFF, and MHD file formats.

Original Segmentation Masks: the 3D models were created using ScanIP by the construction of 3D objects from a series of outlines, or masks, of each object. This was a manual process often requiring subjective decisions when the clarity of the images made the detection of tissue borders challenging. Therefore, we have provided the segmentation masks in 3D Slicer for those that wish to verify or alter the masks for creation of unique models. The raw segmentation masks are available in 3D Slicer as NRRD files. Additionally, the segmentations are available as binary label maps in MHD, TIFF, and .mat file formats.

Segmentation Masks of Smoothed Models: segmentation masks were created from the smoothed and resampled 3D models to enable transverse inspection of the final product in segmentation software 3D Slicer.

Comparison Metadata: includes tables of the initial overclosure amounts tissue geometries as well as comparisons between tissue volumes before and after smoothing and overclosure correction. Comparisons are also made between tissue volumes on the left and right side of the body.

The complete VHM consists of 211 GB of objects and images, and the VHF consists of 144 GB of objects and images. For this reason, the datasets have been split into manageable folders for download. The folders have been separated into those for the Male and Female, and in addition there are separate folders containing:

The segmentation masks are shared in a format compatible with 3D Slicer, which is publicly available at www.slicer.org. The 3D models of the tissues are shared in STL format, which is readable by most open-source and commercial 3D modeling software.

Adding new geometries of the musculoskeletal system of the lower-limb and the torso and upper limbs by other contributors is encouraged and can be added to the dataset by contacting the authors. The authors will check new or revised content for accuracy and completeness and update the folders with full credit of contributors highlighted on the website.