New Publication: Genital interactions during simulated copulation among marine mammals

DiceCT reconstructions of marine mammal copulatory anatomy
CT Reconstructions of marine mammal penises inside vaginas. Images are rendered in sagittal plane for short-beaked common dolphins (D. delphis; top) and harbour seals (P. vitulina; bottom). Two-dimensional volume reconstructions on the left use sharp lung and smooth soft tissue algorithms. Three-dimensional volume renders on the right show erectile tissue in red and non-erectile tissue as transparent.

“We investigated the mechanics of copulatory interactions in marine mammals to determine how morphological diversity of genitalia correlates with function during simulated copulation. The excised penises of deceased male cetaceans and pinnipeds were distended, positioned inside the vaginas of females from the same species, and CT-scanned in situ using diceCT techniques. We found evidence of both congruent and antagonistic genital coevolution between the sexes, depending on the species. Sexual selection forces contribute to the extensive genital morphological variation observed in male and female marine mammals.”

–Lead author, Dara Orbach (@)

Head over to Proceedings B to download the pub!

New Publication: Testing hypotheses of developmental constraints on mammalian brain partition evolution, using marsupials

Digital Brain Model
Exemplar 3D reconstructed marsupial brain: Green/light red, the two olfactory bulbs; orange/blue, cerebral hemispheres; dark green, midbrain; yellow, cerebellum; cherry red, medulla.

“We tested the controversial hypothesis that mammalian brain parts scale conservatively with brain size because of developmental constraints on size-dependent, neurogenetic patterns. Early cell-level constraint should be reflected in conserved patterns of mammalian brain partition growth, but the data required to test this expectation have been unavailable. The hydrogel/DiceCT technique, however, represents a fast way of measuring growth in minute brains, allowing us to provide the first quantification of mammalian brain partition growth. Across three marsupial species, we found no evidence of partition growth regularities with brain size or age although intraspecific growth patterns were very regular. This suggests that species-specific brain growth patterns do exist, albeit not as part of a global pattern of evolutionary  developmental constraint.”

     – Project Leader, Vera Weisbecker 

Visit the the University of Queensland Centre for Advanced Imaging online and read the open access paper at Scientific Reports!

New Publication: Digital dissection of the model organism Xenopus laevis

3D Digital Model of Xenopus
3D model of Xenopus hard- and soft-tissue anatomy, digitally rendered from diceCT scans. Transparent outer layers allow for internal viscera, bone, muscle, and nerves to be seen.

“The African clawed frog Xenopus laevis is one of the world’s most widely used model organisms – yet existing anatomical descriptions are nearly a century old, incomplete and use outdated nomenclature. Moreover, Xenopus exhibits many unusual skeletal and soft-tissue characters compared to well-described “typical” frogs such as Rana. We used diceCT to create a 3D digital dissection of Xenopus, including the skeleton, muscles, nervous, respiratory digestive and reproductive systems. The method was particularly useful in this instance as it preserves 3D topological relationships and permitted dissection of a very small, fragile specimen.


– Lead Author, Laura Porro

Download the dissectable 3D model from the Journal of Anatomy!

Congratulations to Echols and Birch on winning the 2017 Wellcome Image Awards!


B0011001 Microvasculature of the African Grey Parr
African grey parrot with the intricate cervical and cranial blood supply reconstructed in 3D.

Avian vascular injection images by diceCT co-author Scott Echols and colleague Scott Birch were recently recognized as winners of the 2017 Wellcome Image Awards.

Congrats to both Scotts and kudos on the fabulous images—keep up the great work!

New Publication: Quantifying 3D Morphology & RNA from Individual Embryos

Iodine-enhanced CT scan projection of a mouse embryo (E11.5) in 3D (top) and an exemplar embryo RNA integrity analysis after staining and scanning, showing 18S and 26S bands as well as a lower marker (bottom).

“Here we present a method that generates high quality iodine contrasted CT images from embryonic soft tissue. This method has two primary advantages over previous methodologies. First, it allows extraction of high quality nucleic acids following the CT scan, generating a 1:1 correspondence between scan and gene expression or DNA profile. Second, it minimizes the shrinkage artifacts associated with fixation and contrasting. The ability to relate a single sample to its genetic profile will allow study of both partially penetrant models and also increase our understanding of how genotype and phenotype are directly related.”

– Lead author, Rebecca Green (Hallgrímsson Lab)

Go read more at Developmental Dynamics!

New Publication: Three-dimensional visualisation of the internal anatomy of the sparrowhawk (Accipiter nisus) forelimb using contrast-enhanced micro-computed tomography

“A three-dimensional model of the wing musculature of the sparrowhawk (Accipiter nisus) was built using μCT and a 3% iodine-buffered formalin solution to test the ability of the technique for visualising wing musculature and obtaining quantitative data of muscle geometry.  This model allows the identification of the individual muscles comprising the avian wing and can be useful for further biomechanical analysis of flight.”

– Lead Author, Fernanda Bribiesca-Contreras

Go read more about the project at PeerJ!

Transverse μCT images of a sparrowhawk (Accipiter nisus) wing (upper panel)—Columns: (A) Control . (B–F) ∼3% (w/v) iodine-buffered formalin solution after three (B), 10 (C), 15 (D), 18 (E), and 25 (F) days. Rows: (G) Corresponds to brachial area, (H) antebrachial area and (I) the manus (scale bar = 5 mm). Three-dimensional model of the wing muscles of a sparrowhawk (lower panel)—three-dimensional model of the wing muscles of a sparrowhawk reconstructed from CT images of the stained wing after 25 days in a ∼3% iodine-buffered formalin solution (superficial muscles are shown in dorsal (left) and ventral (right) view).



“Tour Through the Brain of Python” Named Winner of the FASEB BioArt Competition

“Tour Through the Brain of Python,” a diceCT visualized video fly-through of a Macklot’s python head by Paul Gignac and Nathan Kley, is a winner in the fifth annual FASEB BioArt Competition!

It’s so important to seize opportunities to share the wonder of discovery with the public. The BioArt images showcase the beauty of scientific research and are a great place to start the conversation —Hudson Freeze, PhD, FASEB President.

The Federation of American Societies for Experimental Biology holds an annual BioArt Competition to help engage Members of Congress and the general public about the immense value of biomedical and bioimaging research in the United States and the need for sustained support of federal funding agencies that facilitate life science and biomedical studies. To celebrate the competition, winning entries will be exhibited at the National Institutes of Health and online at

“Tour through the brain of a python”— Paul M. Gignac, Oklahoma State University Center for Health Sciences, and Nathan J. Kley, Stony Brook University School of Medicine

New Publication: Habitat-specific divergence of air conditioning structures in bird bills

“We used high precision computed tomography (CT) and traditional radiography to study the nasal conchae, complex structures within the nasal cavity that condition air via countercurrent heat exchange. Concha size differed between 2 subspecies of Song Sparrow (Melospiza melodia) that inhabit climatically distinct habitats, suggesting adaptation to local climates. The conchae and external bill are nested structures that were positively related in size and play functionally related roles in thermoregulation, therefore suggesting phenotypic integration. We hypothesize that the typically deeper and wider bill of the dune subspecies has evolved, at least in part, to accommodate larger conchae.”

– Lead author, Raymond Danner

Head over to The Auk to see the the published image sets!

DiceCT sparrow nasal cavities
Frontal cross sections along the bills in 2 Song Sparrows prepared using alcoholic iodine (I2E), illustrating the differences between (A) M. m. atlantica and (B) M. m. melodia. Sections are ordered sequentially, from caudal-most to rostral-most. Within each cross section, the top is dorsal and the bottom is ventral. (Scale bar is 2.0 mm.)