Author Archives: emilianobruner

Digital Endocasts

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Sliding brains

Bruner E. & Ogihara N. 2018. Surfin’ endocasts: the good and the bad on brain form. Palaentologia Electronica 21.1.1A: 1-10.

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Brian Metscher

Following bachelor’s work in applied physics at Caltech and a first career as a research engineer at NASA/JPL, Brian Metscher completed his PhD in the then-new interdiscipline of evo-devo at the University of California, Irvine. He did postdoctoral research on the development and evolution of appendages and teeth at The Natural History Museum (London) and Penn State University, and then served five years as an Assistant Professor in southern Indiana. During the summers he carried out research at Yale University and came to the University of Vienna in 2006, to set up the imaging lab in the Department of Theoretical Biology, where he is now Senior Scientist. He helped to establish X-ray microtomography as an essential method for imaging ex vivo biological samples, especially embryos and invertebrates. His lab is developing new and refined sample preparation and imaging methods, with applications including molecular imaging and imaging of specific cells types. He coordinates a MicroCT Methods Forum. Here a brief interview …

What are the basic principles of these methods mixing histology and digital anatomy?

MicroCT provides 3D images of intact samples at resolutions that overlap with what is achieved by light microscopy of sectioned material. Contrast-enhanced X-ray images give only histomorphological information, so microCT images are a powerful complement to traditional histology, which takes advantage of a vast array of stains with different tissue specificities. MicroCT gives a 3D overview and context for more detailed section-based images from histology (and also electron microscope).

So, you stain specimens before microtomographic scan … what about these staining techniques?

The familiar X-ray images of bones or teeth inside the body are possible because the dense calcium-rich materials absorb a lot more X-ray energy than the soft tissues around them – skin, muscle, and internal organs, which are made up mostly of proteins and water. To make soft tissues clearly visible in X-ray images, it helps to add a contrast agent: this can be a suspension of an iodine- or barium-containing liquid injected or swallowed, as is common in clinical radiology examinations. In the case of non-living samples (ex vivo imaging, most of what I do), the sample can be stained with a substance that actually binds to the tissues and has a higher X-ray absorption. The contrast stains used most often are inorganic iodine, phosphotungstic acid, and (less frequently) osmium tetroxide. None of these is specific to any one tissue type, but they do allow the different tissues and structures to be distinguished clearly in the X-ray images.

What kind of expertise, career, and tools are necessary to work in this field?

As with any kind of biological imaging, it is necessary to have a good understanding both of the biological systems under study and of how the imaging systems actually work. So a strong background in microscopy, histology, and image acquisition and analysis is important. And one must always complement one’s own expertise with good working collaborations with partners in other fields.

What is, at present, the most intriguing current challenge?

We would really like to make microCT imaging more tissue- and molecule-specific. Thus I have collaborative projects to test new staining methods and calibrate their functions in microCT images with histological baselines. And my lab is working on refining the antibody imaging method we published a few years ago to make this a more robust and routine method for 3D imaging of gene expression and other molecular patterns in developmental, comparative, and medical-related research.

Neuroanatomy and Tractography

NATBRAINLAB –  Homepage, Maps, and Blog


Fiorenza L., Bruner E. 2017. Cranial shape variation in adult howler monkeys (Alouatta seniculus). Am. J. Primatol. [link]

Scalable Brain Atlas

The Scalable Brain Atlas (SBA) is a fully web-based display engine for brain atlases, imaging data and ontologies. It allows client websites to show brain region related data in a 3D interactive context and provides services to look up regions, generate thumbnails or download nomenclature – and delineation data … [Atlas] [3Dviewer]


What happens when you donate your brain to science?

Language and endocasts

Since brain does not fossilize, brain endocast (i.e., replica of the inner surface of the braincase, Figure 1) constitutes the only direct evidence for reconstructing hominin brain evolution (Holloway, 1978; Holloway et al., 2004a). In this context, paleoneurology has suffered from strong limitations due to the fragmentary nature of the fossil record and the absence of any information regarding subcortical elements in extinct taxa. Additionally, variation in brain shape and organization (and in the corresponding endocast) is technically difficult to capture, as stated by Bruner (2017a, p. 64): “[…] the smooth and blurred geometry of the brain, its complex and complicated mechanisms, and its noticeable individual variability make any research associated with its morphology very entangled and difficult to develop within fixed methodological approaches.” An emblematic example might be the reluctance of paleoneurologists to consider the sulcal imprints visible on the endocranial surface because of the substantial uncertainties in describing such features in fossil specimens and related debates (e.g., the lunate sulcus in the Taung child’s endocast; Falk, 1980a, 2009, 2014; Holloway, 1981a; Holloway et al., 2004b). In 1987, Tobias even came to the conclusion that “The recognition of specific cerebral gyri and sulci from their impressions on an endocast is a taxing, often subjective and even invidious undertaking which arouses much argumentation” (p. 748) …

[keep on reading this Opinion Article by Amélie Beaudet in Frontiers in Human Neuroscience, published in a special issue dedicated to Language, skull, and brain]

Paleoneuro 2017

Brainstorming today at the Laboratory of Hominid Paleoneurobiology! Talks and chats on several doctoral projects, integrating brain anatomy, functional craniology, vascular morphology and cognitive archaeology. From the left: Emiliano Bruner, Gizéh Rangel de Lázaro, María Silva Gago, Annapaola Fedato, Alannah Pearson, and Sofia Pereira-Pedro.

Hominin biomechanics


Hominin biomechanics

Virtual anatomy and inner structural morphology,
from head to toe
A tribute to Laurent Puymerail

Comptes Rendus Palevol 16 (2017)