Tag Archives: Digital anatomy

Mouse Lemur Brain

The gray mouse lemur (Microcebus murinus) is a small Madagascan primate, averaging 12 cm length and weighing between 60-120 grams. Despite the diminutive size, mouse lemurs are increasingly used in medical studies of Alzheimer’s disease and similar neurological disease processes found in humans. Mouse lemurs often live to 12 years or more in the wild, which combined with torpor (a form of short-term hibernation) may be associated with the longer lifespans. Considering mouse lemurs have prolonged lifespans, it is probably not surprising that they also experience age-related brain atrophy. Nadkarni et al. (2019) address the absence of a dedicated mouse lemur brain atlas through in-vivo MRI scanning 34 mouse lemurs, investigating age-related brain atrophy and the neuroanatomy of Microcebus murinus in a comparative context. Results showed that most of the cerebral cortex was affected with age-related brain atrophy including the primary visual cortex and, although the remainder of the primary sensory areas were unaffected by atrophy, an even higher amount of atrophy was found in the sub-cortical brain regions including the thalamus, hippocampus and amygdala. All previous studies of mouse lemur neuroanatomy have been conducted with histological atlases. However, Nadkarni and colleagues compared mouse lemur cerebral to cortical volumes using high-quality MRI, finding that contrary to histology studies, mouse lemurs had similar cortical to cerebral volume indices to other primate species and were not to be considered a “lesser primate” species as has been previously argued. The proportion of cerebral white matter was the highest in humans, before a continual decrease in macaques and smaller monkeys with the lowest white matter volumes observed in mouse lemurs. The trend for increasing white matter volumes in primates, culminating with the highest values in humans, has often been argued as necessary for reinforcing intra-cerebral connectivity, hypothesized as an important process in primate brain evolution.

Included with this study of mouse lemurs, Nadkarni and colleagues also produced an accompanying MRI in-vivo brain atlas which includes 120 labelled brain structures specific to Microcebus murinus which to-date, has been unavailable. The accessibility of a brain atlas specific for mouse lemurs removes the time-consuming process of manual MRI segmentation, allowing quick and direct comparison of brain regions with other primates for a comparative evolutionary context and in medical research for Alzheimer’s disease.

Alannah Pearson


Automated digital tools

Since the early 2000s, the expansion of digital anatomy tools has been aided by advances in computational power and accessibility of medical imaging such as Computed Tomography (CT). The greater accessibility to digital imaging of fossil material has allowed the reconstructions of inner cranial cavities (endocasts), sinuses cavities, and dental reconstructions of the enamel-dentine junctions (EDJ) of fossilized teeth. Despite great accessibility, the segmentation processes used to generate digital reconstructions of inner cavities remain time-consuming and require specific expertise in computer analysis, anatomy, digital imaging.

Profico et al. (2018) provide two fully-automated digital methods to minimize these time-consuming digital segmentation tasks. Both of these methods rely on point-of-views (POVs) to delineate a region-of-interest (ROI). In the CA-LSE method, POVs were located outside a ROI and all areas beyond are subtracted from the final reconstruction. In contrast, the AST-3D method relies on a ROI defined by POVs placed inside a cavity and all external areas, subtracted from the final reconstruction. While both methods are similar and can be used to generate reconstructions of the inner cavities, each method has slightly different benefits. Profico and colleagues conducted a comparison of both methods to determine strengths and weaknesses of each approach. While both of these methods are available through the Cran R network, two different R packages were tested: Morpho and Arothron.

Results indicated that in the Morpho package, CA-LSE had no restrictions on where POVs could be placed, but using AST-3D method in Morpho, POVs had to be manually placed inside the internal cavity for successful reconstruction. In the Arothron package, CA-LSE method allowed fully-automated placement of POVs outside the ROI surface, however, the AST-3D method a ROI must be defined by manually placed POVs within the inner cavity. In general, accuracy of the AST-3D and CA-LSE methods were determined by each method, with AST-3D more reliable generating reconstructions of inner cavities (such as endocasts), while the CA-LSE was more suited to reconstructions of outer structures (such as skulls).

Although, automatic approaches offer time-efficiency and often allow larger sample sizes to be more quickly processed, many fossilized skulls are highly fragmentary and automated methods remain limited when fossilized remains are partially or entirely matrix-filled with anatomical and digital expertise still requiring manual segmentation. In these complex scenarios, further fine-tuning of automated methods would be invaluable with inclusion of fully-automated, semi-automatic and manual options.

Alannah Pearson

Digital Endocasts

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Close-range Photogrammetry or Surface Scanner?

postRecently, Evin et al. 2016 have published a study comparing the accuracy of the three-dimensional reconstruction of five wolf crania using both photogrammetry and high-resolution surface scanner. For the photogrammetric images acquisition, they used an 8-megapixel (DSLR) Canon EOS 30D camera, mounted with a Canon EF 24–105mmf/4 L IS USMlens. The scanner-based 3D models were created using a Breuckmann StereoScan structured light scanner (http://www.breuckmann.com). The resulting 3D models were compared first through visual observation, and second with the computation of a mesh-to-mesh deviation map. The pairs of models were spatially aligned (using a least-square optimisation best-fit criterion), followed by a 3D landmark-based geometric morphometric approach using corresponding analyses. The results show that photogrammetric 3D models are as accurate in terms of coloration, texture, and geometry, as the highest-end surface scanners. Minimal differences between photogrammetric 3D models and surface scanner-based models have been only identified on intricate topological regions, such the tooth row. Photogrammetry is becoming a common tool in archaeological and anthropological research. The major advantage of this technique is the speed and ease of image acquisition and reconstruction. Photogrammetry is an equally good alternative and less expensive than other more common techniques, such as structured light or surface scanners. In terms of archaeological samples conservation, photogrammetry could be in the future an excellent alternative to provide accurate replica models that can be widely accessible for research, without affecting the original collections.

Gizéh Rangel de Lázaro

Structural MRI artifacts

Magnetic resonance imaging (MRI) is a valuable and increasingly used method for studying brain anatomy as it allows large-scale, high-quality in vivo analyses. However, some artifacts might influence the digital results, and thus require cautious interpretation. In a recent review, these issues are addressed along with possible solutions. First, we need to keep in mind that the images acquired are not mere photographs of the brain, but reflect some biophysical properties of the tissues, by measuring the radio-frequency signals emitted by hydrogen atoms (present in water and fat) after being excited by magnetic waves. Thus, MRI is an indirect analysis of the brain anatomy and depends greatly on specific tissue properties. Second, researchers can choose from a variety of methods, depending on the aim of the survey. Macrostructure, i.e. the size and shape across voxels, can be studied through manual volumetry or automatic segmentation, voxel- or deformation-based morphometry, surface- based algorithms, or diffusion tractography. Microstructure, i.e. within-voxel contents, is usually analyzed through diffusion MRI, but also magnetization transfer imaging, or quantitative susceptibility mapping.

When making inferences on the biological significance of the outputs, the researcher must account for the possible digital artifacts. These can occur both during image acquisition and processing and can be subject-related and methodological-related. A common problem is subject motion, which might contaminate or influence the results, as the amount of motion varies with other factors influencing brain changes (age, sex, and disease status), or can even correlate with a specific effect being studied. For instance, motion induces gray matter reduction, which might be perceived as brain atrophy. Subject motion is unavoidable, but its influence can be reduced by using a motion detector during acquisition, or by estimating the amount of motion allowing statistical adjustments, also useful to  detect outliers. The difficulty in manipulating the magnetic and radio-frequency fields might also introduce deformation. The main magnetic field should be spatially uniform, but it is dispersed by brain tissue while concentrated by air. This can be partially compensated by applying additional fields. The radiofrequency field is not homogeneous, which affects MRI contrast and intensity. Combining multiple transmit coils might help reduce this caveat, although the contribution and sensitivity of each coil must be taken into account when processing the image.

A particular case that can affect estimates of cortical volume and thickness is the difficulty in discriminating the dura and gray matter due to the similar intensity and anatomical proximity. In this case,  MRI parameters can be manipulated in order to increase the contrast between these tissues, without reducing the contrast between gray and white matter. Individual variability in folding patterns is a further major issue in voxel-based morphometry studies because it complicates the mapping of correspondences between subjects. Registration might be enhanced by analyzing regions with larger variation to find possible anatomical alterations, aligning cortical folding patterns to locate corresponding areas, and mapping sulcal changes to improve sulci identification. Finally, researchers should continuously keep track of the constant advances and innovations in the field. The authors conclude acknowledging the importance of structural MRI when coupled with other biological information, like genetic expression (Allen Brain Atlas), cytoarchitecture (JuBrain), and cognitive associations (Neurosynth).

Sofia Pedro

Open-access 3D morphological datasets

morphosourceMorphoSource, is a dataset project for storing, collaborative sharing, and distribution of microCT scans, 3D surface rendering, and 2D digital imaging. Its main goal is to provide rapid access to as many researchers as possible, large numbers of raw microCT data, and surface meshes representing vouchered specimens. The site is active since April 2013 and now hosts almost 5000 files, including ‘raw’ microCT volumetric data, mesh files  from laser scans, and 2D digital photographs (file formats include tiff, dicom, stanford ply, and stl). MorphoSource, allow to download a world-wide repository-vouchered digitalized specimens from 48 institutions (American Museum of Natural History; Muséum National d’Histoire Naturelle; Natural History Museum Vienna, see more in Institutions). Currently the amount of information related with genus Homo is limited to Homo sapiens; however the site dataset is growing rapidly, and in the future it will be an interesting source of data for Paleoanthropologists too.

Gizéh Rangel de Lázaro

Digital reconstruction

piece“Replacement of Neanderthals by Modern Humans” (RNMH) is a project aimed at investigating possible cognitive and behavioural  differences between these two human groups. I belong to the team coordinated by Naomichi Ogihara at the Keio University, and we have now published a review article  about digital reconstruction of fossil crania and analysis of their brain morphology. As engineers, we are trying to reconstruct the brain anatomy of Neanderthals and early modern humans according to numerical approaches and mathematical models. Soft tissues do not fossilize, so we are trying to provide a spatial estimation of the brain anatomical organization. As a first step, restoration of the original cranial morphology is necessary, because fossil remains are often fractured, fragmented, and deformed because of the taphonomic and diagenetic processes. Digital tools and virtual simulation procedures are used to achieve a more precise and objective morphological reconstruction. Mathematical approaches are applied in such computational techniques. For example, cranial fragments are assembled based on smoothness (minimizing fitting error) of their joints. The deformation is corrected by affine transformation or thin-plate spline (TPS) function based on bilateral symmetry. Missing parts are interpolated by several mathematical approaches. This new paper reviews the current status of methods in computed anatomy, and it presents an overview on digital reconstruction of fossil crania, aimed at supplying computed methods to estimate their brain morphology.

Hideki Amano

Mapping the cranial vault

Thickness and density

More on vault thickness. As we commented in the previous post, the cranial vault can be divided in three layers: external table, diploe and internal table. Many previously studies provided information about skull thickness and density, but generally were based on a scarce number of measurements and with limited small sample size. Digital anatomy allows to go beyond many limits and constraints when working on this topic. Arne Voie and coauthors published a study based on parametric mapping and quantitative analysis of the human cranium. This team from San Diego, California, working mainly on neuroscience and radiological investigations, described how the thickness and density of the human skull changes depending on the anatomical regions (frontal, temporal, parietal and occipital bones). Measurements were computed on 51 dried crania of modern humans (males and females, ranging from 53 to 97 years old) and were analyzed by using 2000 points positioned on the three layers. Thickness and density distribution were calculated by using an algorithm to detect dense point of both extra and intra cranial boundaries and the lower density values of the diploic layer. The density results were mapped parametrically on each cranium to display their thicker areas and their distribution. The analysis evidenced a marked variation among the specimens. The thicker regions of the skull, namely the parietal, occipital, and frontal bones, have a mean value of 10.14 mm. In almost half of the sample the denser areas are the coronal and sagittal sutures, especially in their meeting point, while in the rest of the sample the density varies widely. The study cannot evidence sexual differences in both thickness and density.

Gizéh Rangel de Lázaro



Radiopaedia, skulls and brains, bones and vessels, a very nice imaging source on Tumblr!