New Publication: Best Practices for Digitally Reconstructing Endocranial Casts

CT images and cranial endocasts based on the cranial osteology of extant and fossil specimens as well one prepared using diceCT imaging.
CT images and cranial endocasts based on the cranial osteology of extant and fossil specimens as well one prepared using diceCT imaging.

“The use of digital endocasts (casts of the cranial cavity, which approximate the morphology of the brain) to study neuroanatomical patterns in the deep history of vertebrates has become important and pervasive in the past several years. Up to this time, however, no “best practices” for digitally constructing these casts had been established. We brought together a large number of researchers who are actively working on comparative neurological studies involving endocasts to help standardize such techniques. It is our intent that this paper will stimulate discussion and empirical testing of methods, so that scientific consistency can be achieved throughout this research community.”

–Lead author Amy Balanoff

Head over to the Journal of Anatomy to read the pub!

The Austin Working Group

The Austin Working Group Meeting, April 2–3 at The University of Texas, Austin
Austin Working Group members: (from top left) Larry Witmer, Juan Daza, Henry Tsai, Johannes Müller, Matthew Colbert, Zhiheng Li, Julia Clarke, Scott Echols, Paul Gignac, Nathan Kley, Nele Herdina, Philip Cox, Daniel Paluh, Catherine Early; (from bottom left) Ian Cost, Elizabeth Glynne, Casey Holliday, Courtney Orsbon, Samer Merchant, Ashley Morhardt, Don Cerio, & Monte Thies. (Not pictured are Mark Henkelman and Brian Metscher.)

A tremendous “Thank you!” goes out to the members of the Austin Working Group, whose efforts throughout 2015 have resulted in the digital resources published here as well as upcoming conference workshops and symposia. Together, we seek to grow the diceCT community and advance 3-D soft-tissue imaging well into the future.CB60vhyUkAABl8G.jpg-large

Thanks also to the National Science Foundation, The University of Texas at Austin, and UT CT Lab for their financial and institutional support.

The international, multi-institutional effort that started us off!
The Austin Working Group met for two days in April to discuss the state of the art for iodine-based contrast enhancement of X-ray μCT images. What emerged from that meeting was a set of standards and protocol recommendations as well as a strong desire to grow this nascent community.

DiceCT Symposium at the 2016 International Congress of Vertebrate Morphology

Two dozen speakers are schedule to present in our diceCT symposium at ICVM in 2016.
Two dozen speakers are schedule to present in our diceCT symposium at ICVM in 2016.

Diffusible iodine-based contrast-enhanced computed tomography (diceCT) and related imaging techniques for research in evolutionary morphology

Organizers: P. M. Gignac1*, A. N. Herdina2, N. J. Kley3, A. Morhardt4, J. A. Clarke5, and M. Colbert5

The ability to visualize hard tissues (e.g., bone, dentine, enamel) rapidly in three dimensions using X-ray computed tomography (CT) has been one of the most important advancements in the field of vertebrate morphology in the last half-century. Until recently, however, comparably valuable advances in soft-tissue imaging have been difficult to realize fully due to the inherently low X-ray absorption of non-mineralized structures. Pioneering work in this area has demonstrated that Lugol’s iodine (I2KI) is a highly effective contrast agent for rapidly differentiating many types of soft tissues (e.g., epithelial, muscular, and neural structures) in micro computed tomography (μCT) images. Vertebrate morphologists have become a driving force in advancing this technique and utilizing the remarkable data generated from it to reconstruct phenotypes and functional anatomy in three and four dimensions.

Given the broad potential for iodine-enhanced CT imaging to become a major tool for soft-tissue reconstruction in vertebrate morphology, we will hold a symposium at the 2016 ICVM meeting to exhibit the wide range of taxa and questions that can be examined using these approaches. Through our symposium, Diffusible iodine-based contrast-enhanced computed tomography (diceCT) and related imaging techniques for research in evolutionary morphology, we will feature the newest and ongoing applications of contrast-enhanced three-dimensional (3-D) imaging already being undertaken by researchers within the International Society of Vertebrate Morphology. We further propose to hold a student-focused, combined poster session with the Hartstone-Rose and Marchi symposium on muscle functional morphology, to bridge the related techniques of our respective presenters. Our goal is to spur the further adoption of these methods by vertebrate morphologists. We will achieve this by (1) highlighting recent methodological advances in contrast-enhanced CT and μCT imaging, (2) demonstrating active research that integrates diceCT and related imaging techniques into toolkits addressing macroevolutionary questions, and (3) generating discussions of future directions and the long-term place for contrast-enhanced imaging in the study of extant vertebrates. We have assembled a diverse group of speakers who have enthusiastically agreed to participate in this symposium. They include well-established researchers, emerging early-career scientists, and graduate students in the fields of functional morphology, biomechanics, phenotypic integration, and vertebrate paleontology, whose academic contributions have already brought important insights to evolutionary biology. Demonstration of the high-level inferences that can be garnered with diceCT will spur collaborations among labs already exploring this powerful new tool with those who are considering how to apply it to their own research questions.


Poster Symposium

  • Green — Physiological examination of ratite orthopedic disorders and soft- tissue visualization via micro-CT
  • Herrel — Contrast-enhanced versus phase-contrast imaging: costs and benefits of different methods
  • Holliday — DiceCT and its applications for understanding the reptile musculoskeletal system


Introduction & Neurological Visualization

  1. Gignac — DiceCTing the future: new horizons for 3-D visualization of vertebrate morphology (30 min)
  • Weisbecker — Using the STABILITY protocol prior to IKI-staining to provide the first accurate, in situ quantification of mammalian brain proportion scaling using marsupials (15 min)
  • Watanabe — Mind the Gap: ontogenetic shape differences between brains and endocasts in archosaurs (15 min)
  • Hughes — Incorporating diceCT into multi-scale structural studies of the brain for highly divergent lineages of acrodont Lizards: validation of preservation methods conducted in the field (15 min)

Functional Morphology

  • Gold — Applying diceCT to PET: new tools for correlating morphology to function in living animals (15 min)
  • Charles — Musculoskeletal modelling and simulations of the mouse hind limb during locomotion: the role of high-resolution scanning and contrast Imaging (15 min)
  • Lautenschlager — The evolution of the mammalian jaw adductor musculature – inferences from soft-tissue imaging of extant taxa (15 min)
  • Cox — Masticatory muscle anatomy of African mole-rats revealed by diceCT (15 min)
  • Orsbon— Integration of diceCT with XROMM and fluoromicrometry enhances functional morphology and biomechanics research: a case study of the macaque (Mammalia: Primates) feeding apparatus (15 min)

Descriptive Anatomy

  • Stanley —Contrast-enhanced CT provides insight into amphibian lingual morphology (15 min)
  • Pardo —Studying metamorphosis of the cranial musculoskeletal system in the axolotl using contrast-mCT (15 min)
  • Porro —Contrast-enhanced micro-CT imaging of fish and frogs: digital dissections and biomechanical applications (15 min)
  • Yohe —The curious case of the vomeronasal organ in bats: genetics asks questions only anatomy can answer (15 min)
  • Vander Linden —Comparative morphology of bat cranial muscles using contrast enhanced micro-CT imaging (15 min)


Advancements and Infrastructure for Contrast-enhanced Imaging Techniques

  • Herdina — Advantages and difficulties of alcoholic iodine staining for correlative 2-D and 3-D micro-CT imaging and histomorphology in bat developmental studies (15 min)
  • Mahlow — DiceCT and the staining of old museum specimens, exemplified by the analysis of venom glands in viperid snakes (15 min)
  • Morhardt — Diffusible iodine-based contrast-enhancement of large, post-embryonic, intact vertebrates for CT scanning: staining, destaining, and long-term storage (15 min)
  • Li — An evaluation of the efficacy and mechanism of contrast-enhanced X-ray computed tomography for avian cranial material utilizing iodine through experimental and simulation approaches (15 min)
  • Starck —The publishing and archiving of microscopic anatomy (15 min)



1*Department of Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, OK, USA (corresponding organizer:

2Department of Theoretical Biology, University of Vienna, Vienna, Austria

3Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY, USA

4Department of Biomedical Sciences, Ohio University, Athens, OH, USA

5Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA