“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 FASEB.org.

“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.)

VA-044 Azo Initiator Supply for STABILITY

va-044For those diceCT users working STABILITY protocols into your specimen preparation regimes, we’ve been hearing reports that your thermally-triggered initiator, VA-044 (2,2′-Azobis[2-(2-imidazolin-2-yl)propane]dihydrochloride), may be difficult to source. It tends to be sold in larger volumes than researchers practically require for STABILITY, which has made it difficult to purchase while leaving much of the chemical unused on researcher’s shelves.

Dr. Vera Weisbecker (University of Queensland, Queensland, Australia) has recently offered to share some of her supply with STABILITY users, who might not be able to get a hold of it from Wako Specialty Chemicals or elsewhere. Please email her directly if you are interested. 

We, @DiceCT, would like to offer an enormous thank you to Dr. Weisbecker for her generosity and openness, in particular, as well as for advancing STABILITY for our larger community!

DiceCT on Display at the Royal Society of London Online


A diceCT visualized ratsnake head and brain is a finalist in the 2016 Royal Society of London Scientific Photography Competition! This piece and many other contributions of remarkable scientific artwork are now part of a display at the Royal Society of London Online.

“The cranial anatomy of a diceCT imaged ratsnake in frontal view” by Nathan Kley and Paul Gignac. Ratsnake (genus Pantherophis) head in frontal view, prepared using diffusible iodine-based contrast enhanced computed tomography (diceCT) imaging, in which an iodine staining solution acts as a contrast agent that non-destructively renders soft tissues visible in X-ray micro-CT scans. The specimen was imaged using a GE Phoenix v | tome | x micro-CT scanner at 29.5 microns. Soft tissues including the brain and its internal structures, spinal cord, optic chiasm, roots and branches of cranial nerves, jaw and neck muscles, glands, nasal epithelia, cranial bones, and integument can all be clearly visualized simultaneously. (Image contrast and brightness were modified to render the background fully black and the neck was cropped to fit the image frame.)

The competition celebrates the power of photography to communicate science and the role images play in making science more accessible to a wide audience. To view featured photos at the Open House exhibition (9/17–9/18/2016), visit The Royal Society of London.

New Publication: Comparison and Evaluation of the Effectiveness of Two Approaches of Diffusible Iodine-Based Contrast-Enhanced Computed Tomography (diceCT) for Avian Cephalic Material


Screen Shot 2016-08-24 at 11.39.46 AM
Sagittal sections of the two tinamou heads processed using I2KI-formaldehyde (A) and I2E (B), respectively. Black arrows highlight the staining effect on the spinal cord; white arrows highlight the differential penetration of iodine in the two approaches (inset 3-D renderings for each specimen show the section positions).

I2KI-formalin (iodine-potassium iodine-formalin) treatment can obscure the natural X-ray contrast of the bone due to neighboring soft-tissues during staining of avian cephalic material. By contrast, we found the I2E (iodine-ethanol) treatment can increase the X-ray opacity of not only soft tissues (e.g., muscles), but also the bone. Mathematical simulations suggest that remarkably different results from I2E and I2KI-formalin staining are due to different partition coefficients and retardation factors of tissues, fixation effects, and distinct iodine diffusion and sorption patterns. We also found a clear positive relationship between glycogen concentration and grayscale values measured within muscle, epithelia, nervous tissues, and glands regardless of the staining solution used.

–Lead Author, Zhiheng Li

Head over to the Journal of Experimental Zoology to download the pub!

Get Your Brights Brighter & Darks Darker: CLAHE + diceCT

By Aki Watanabe (@akiopteryx)

Contrast limited adaptive histogram equalization (CLAHE) is a procedure for enhancing local contrast in an image or stack of images. In contrast to standard histogram equalization that applies single formula for enhancing contrast across the entire image, CLAHE applies multiple equalizations within partitions of an image, resulting in more localized and subtle contrast enhancements. This results in digital contrast enhancement that is not dominated by overly deep blacks or excessively bright whites.

For diceCT, CLAHE is very useful for improving edge recognition for digitally segmenting regions of interest (ROI) based on your CT data. It is particularly helpful when applied to sub-optimally stained specimens.

CLAHE is implemented in FIJI (ImageJ) and the script is available freely and openly. To perform it on a stack of CT images:

  1. Drag and drop the folder that contains a stack of CT images into FIJI (download here: https://fiji.sc). Wait until FIJI reads in the entire image stack.
  2. Copy the CLAHE script from the “Tips” section on the website.
  3. In FIJI, go to “Plugins” > “New” > “Macro”. A new window will open. In the text field, paste the CLAHE script.
  4. Select “Run”. One can specify the “block size,” “histogram bins,” and “max slope” parameters (the details of which are outlined on ImageJ.net), but I have found that the default parameters do a fine job.
  5. Once CLAHE has gone through the entire stack, save the new image stack in a different folder to keep the original CT image stack intact (you never know when you’ll need them).
  6. In CT data processing program of your choice (e.g., Avizo, VGStudio), read in the modified image stack.

Here is a before and after example to illustrate how CLAHE enhances diceCT images.


Screen Shot 2016-08-01 at 6.22.53 PM
DiceCT, two-year old Alligator mississippiensis head in transverse views (left) unmodified, and (right) filtered using CLAHE.

CLAHE processes image stacks fairly quickly, so I recommend trying it with all diceCT image stacks. Generally, it improves edge recognition for all 3-D rendering programs, thus, greatly reducing the time spent on segmenting ROIs. As mentioned above, CLAHE is particularly useful for sub-optimally stained specimens, which is helpful when one cannot devote time or reserve frequent CT scanning sessions for checking and optimizing the stain concentration and duration.

Potential issues with CLAHE include the increase in file size associated with CT data from having both original and modified image stacks. In addition, CLAHE may accentuate unwanted artifacts like beam hardening, so there is further motivation to minimize such scanning artifacts.

Those interested in learning more about the method can visit Wikipedia and read through the original article (Zuiderveld, 1994).

A modified STABILITY protocol for accurate retrieval of soft-tissue data from micro-CT scans of IKI-stained specimens.

Alison Carlisle1, Vera Weisbecker1*,

1School of Biological Sciences, University of Queensland.
*For correspondence, e-mail: v.weisbecker@uq.edu.au


Modified from Wong, Spring, & Henkelman (2013)

Ingredients and Proportions:

  • ice-cold 4% (wt) formaldehyde (PFA) (We used freshly made solution. Also, note that commercial formalin solutions often contain methanol, which may cause shrinkage.)
  • 4% (wt/vol) acrylamide/bisacrylamide (hydrogel monomers) (We used a pre-made solution of 38% Acrylamide and 2% Bis-acrylamide by Amresco.)
  • 0.25% (wt) VA-044 (thermally-triggered initiator) (This one can be hard to find; we source ours from Wako Australasia.)
  • 0.05% (wt/vol) of saponin (This is useful if you want to increase specimen permeability, or if the specimen is large.)

Mix all ingredients together. Ingredients should be kept on ice during preparation of the solution to prevent premature polymerisation.


(1) Incubation

Immerse specimens in hydrogel solution for 1-2 weeks at 4° C. Larger specimens should be immersed for longer, and specimen type may be important too (e.g., lizards probably take longer than tadpoles). Users should be aware that the immersion time here is longer than for the original STABILITY protocol (Wong et al., 2013). This may be due to longer fixation in formalin, which seems to use up some biomolecule binding sites.

(2) Curing

Any type of vegetable/nut/canola oil can be used for curing (approximately 3 ml). Carefully pour the oil on the surface of the hydrogel solution to form an airtight layer. Some researchers use a vacuum pump nitrogen replacement step, but we found the oil easier. The vials are placed in a water bath set at 37º C for three hours, triggering polymerisation of the gel.  After polymerisation, remove excess gel (now solidified) with clean gloves and lint-free wipes, revealing the specimen as a gel/tissue hybrid. Specimens were then placed directly into iodine solution.

(3) Staining

Some potential issues: This brain was very large (~140g) and did not stain throughout; fridge staining, however, may have improved this. Also, note the high density “pockets” that occur much less frequently if staining is done in the fridge.

For staining we used 1.75% IKI solution, for about 30% longer than we would normally stain—but this depends on specimens and needs to be refined a bit more. Lower-concentration solutions may yield even less shrinkage. Aki Watanabe (pers. comm.) reported slower uptake of iodine at room temperature, which he found advantageous for a more controlled stain. We also found that staining in the fridge reduced the number of high-density “pockets” of iodine producing interference during scanning.


Stain visualization and reconstruction of specimen in 3-D, using Mimics by Materialise.

Please feel free to use our protocol. If you do so, we would appreciate a citation:

Carlisle, A., Weisbecker, V. (2016) A modified STABILITY protocol for accurate retrieval of soft-tissue data from micro-CT scans of IKI-stained specimens. Published online at https://dicect.com/2016/08/09/stability/, August 09, 2016.



Wong, M. D., Spring, S., & Henkelman, R. M. (2013). Structural stabilization of tissue for embryo phenotyping using micro-CT with iodine staining. PloS ONE, 8(12), e84321. [doi:10.1371/journal.pone.0084321]

Method presented at the 11th Meeting of the International Congress on Vertebrate Morphology


New Publication: Enhanced X-ray absorption for micro-CT analysis of low density polymers

Screen Shot 2016-07-14 at 2.22.07 PM
3-D rendering based on a μCT scan (A) alongside an SEM micrograph (B; 1000x magnification) of a biopolymer composite stained with 1.5 wt.% iodine and fixed with HMDS.

“μCT scanning of low density porous polymer scaffolds leads to insufficient imaging ability due to poor contrast. In order to enhance their X-ray absorption, one might trial several approaches using contrast agents. This methods paper is aimed at guiding scientists in applying the most appropriate contrast enhancement method for CT imaging of such materials, by reporting both the positive and the negative results. Iodine staining coupled with chemical drying was the most efficient approach, allowing for contrast enhancement, morphology preservation, and high resolution all at once.”

– Lead Author Livia Crică

Read the paper in the Journal of Biomaterials Science, Polymer Edition!



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

  • 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: paul.gignac@okstate.edu)

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

New Publication: Diffusible iodine-based contrast-enhanced computed tomography (diceCT)—an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues


diceCT eclectus parrot head
Cover: An eclectus parrot (Eclectus roratus) stained by C. M. Holliday (University of Missouri) and micro-CT scanned by L. M. Witmer (Ohio University) according to the diceCT protocol presented by Gignac et al. (pp. 889–909) that reveals unprecedented soft-tissue detail in CT scanned specimens.

“Use of iodine as a contrast agent for computed tomography visualizations has been a growing area of research for the last several years. In this open access study we provide a summary of the diceCT literature and synthesize the elements of successful approaches: we analyze factors that govern success at each step of the diceCT imaging pipeline; we recommend a standard for reporting details of specimen preparation, storage, and imaging that will be pivotal to the repeatability and broader adoption of diceCT going forward; and we discuss cutting-edge applications and future directions for diceCT techniques. We anticipate robust growth within the diceCT community and the realization of new horizons in contrast-enhanced imaging—and it is our explicit purpose to spur the adoption of this relatively nascent approach by the morphology community as a whole.”

–Lead Author Paul Gignac

Access the paper in the Journal of Anatomy!