SpiceCT: Contrast Enhancement Before Your Very Eyes

“Is iodine perfusable?”

This is one of the most frequently asked questions by the diceCT community, and the Witmer Lab at Ohio University has answered: “Absolutely!”

Comparison of diceCT- and spiceCT-imaged cormorants in frontal view—note the drastic difference in staining time for comparable soft-tissue contrast.

SpiceCT (selectively perfusable iodine-based contrast-enhanced CT) is particularly good at staining large specimens very rapidly. Iodine is perfused through the arterial system and across capillary beds, staining soft tissues nearly instantaneously and allowing for targeting regions of interest based on blood supply.

The Witmer lab recently presented their new protocol at the Society for Integrative and Comparative Biology meeting in San Francisco on 4 January 2018 and are now sharing that poster widely on FigShare. Download the poster, and add a new tool to your arsenal!


Thank you to authors Witmer, Porter, Cerio, Nassif, Caggiano, Griffin, and Ridgely. Find more of their work on the Witmer Lab homepage and on Twitter.



New Publication: Parallel Saltational Evolution of Ultrafast Movements in Snapping Shrimp Claws

3D digital reconstructions of the musculature and joint mechanism in shrimp snapping claws; diceCT models alongside confocal imaging, high-speed video, and kinematic experiments helped to elucidate how the extreme performance of crustacean claws came about.

“Does dramatic functional change depend on dramatic morphological change? Kaji et al. used contrast-enhanced micro-CT and confocal imaging, high-speed video, and kinematic experiments with select 3D-printed models, to reconstruct the evolutionary changes in form and function that yielded spectacular snapping claws from simple pinching claws in two shrimp families.  They discovered that two novel claw-joint types — a slip joint and a torque-reversal joint — preceded the evolution of snapping.  They also found that the evolutionary transitions slip joint ➔ torque-reversal joint ➔ snapping occurred in both shrimp families studied.  These results show how subtle changes in joint-form yielded dramatic changes in claw function (e.g., closing speed) during the evolution of snapping claws.”

– Lead author, Tomonari Kaji (@)

See more of Dr. Kaji’s research online and head over to Current Biology to read the pub!

New Publication: 3-D mammalian tooth development using diceCT


Histology (a, e), 2D diceCT sections with outlines of layers (b, f) and anterior (c, g) and apical (d, h) views of 3D models of enamel knots developing within upper canine (a–d) and lower dp3 (e–h). Scale bars = 100 μm. (See figure legend in the web version of this manuscript for interpretations of colored regions.)

“We applied the diceCT technique to image, in three dimensions, a mammalian tooth development pattern, using embryos and pouch young of the tammar wallaby (Macropus eugenii). This enabled individual tissue layers within developing teeth to be clearly distinguishable and even allowed us to image single-cell layer tissues with higher magnification sub-volume scans. Within the same scan we could 3D-visualise both the soft and hard tissues present at various stages through tooth development, including the primary and secondary dental laminae, as well as first and second generations of teeth. With these contrast-enhanced scans, we produced 3D models of in-situ tooth development, demonstrating the enormous potential to visualise this and other organogenetic patterns using this technique.”

– Authors Qamariya Nasrullah (@), Marilyn Renfree, & Alistar Evans 

Head over to the Archives of Oral Biology to read the pub and the Evans EvoMorph Lab webpage & Twitter to see more!

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!