Dr. Jaimi Gray

top left - front page of the PDF of the paper entitled " Establishment of Aquatic Rio Cauca Caecilians, Typhlonectes natans (Fischer 1880) (Gymnophiona: Typhlonectidae), in Florida, with Notes of their Relative Abundance, Distribution, and Natural History. Top right - a 3D rendering of a CT scan of a caecilian, with bone colored skeleton and transparent body, with fish bones inside (rendered in blue) and radiodense digested food (rendered in yellow). Bottom - photograph of a live Rio Cauca Caecilian.

It appears that these aquatic caecilians are doing pretty well down there and definitely reproducing in Miami, with a whopping 115 individuals collected using cans of chicken vienna sausages 🌭

A 3d rendering of a CT scan of two Rio Cauca caecilian with transparent body and bone colored skeleton, showing baby caecilians inside, each rendered in a different color. There are three baby caecilians in the top individual, rendered in green, pink, and purple, and one baby caecilian (rendered in blue) plus one unidentified object (rendered in yellow) in the second individual.

I had so much fun being part of this project! On my scheduled scanning days @ UF Coleman would hand me a bucket of caecilians collected from the Tamiami canal. I put each under the X ray beam to look for babies or interesting food items. If I saw anything of interest, I CT scanned them.

A 3d rendering of a CT scan of a Rio Cauca caecilian with transparent body and bone colored skeleton, showing 7 baby caecilians inside, each rendered in a different color - counter-clockwise from tail to head - red, orange, yellow, green, light blue, dark blue, purple.

Say hello to Florida's newest established species, Typhlonectes natans - the Rio Cauca Caecilian! You can read about their relative abundance, distribution, & natural history, in our brand new paper:

journals.ku.edu/reptilesanda...

Here is one individual I CT scanned that had 7 babies inside!

3D rendering of a diceCT scan of a coiled green tree python, rendered in bright green. Slightly overlapping is a 3D rendering of the python's skeleton, rendered in a light brown color.

It's #WorldSnakeDay so here is a green tree python I CT scanned for #oVertTCN 🐍

Get the datasets (both #diceCT and regular CT) on MorphoSource: www.morphosource.org/concern/biol...

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Now Jaimi Gray is up! "The Diffusion Diaries: Using diffusible iodine-bases contrast-enhanced Computed Tomography for High-throughout imaging of 3D anatomy of natural history specimens" #JMIH25 #ASIHin3D

Display slide that reads "Joint meeting of Ichthyologists and Herpetologists Saturday July 12, 2025 / 10.30am - 10.45 Session with big attendance '28.1 | the Diffusion Diaries: using Diffusible Iodine-Based Contrast-Enhanced...' Jaimi Gray"

Catch me at 10.30am in the Science in 3D #ASIHin3D symposium at #JMIH25 today! Amphibians 🐸 Reptiles 🦎 CT scanning ☢️ Iodine 🧪 Anatomy 🧠

Picture of a powerpoint slide that reads "Science in 3D"

#ASIHin3D begins! An absolute banger line up of speakers today (including me @ 10.30). LET'S GO 🥳 #JMIH25

"Early bird gets the sperm" direct quote by @drscanley.bsky.social during Katherine Greenwald's amazing keynote on unisexual salamanders... And so #JMIH25 begins

Alert for those also arriving to St Paul for #JMIH25 on very little sleep and are also into sharks (I think there's a few of you 😉), the Lost Fox has a very strong coffee option called the "Hammerhead".... 🦈

Got it!

A coffee cup sitting on a table at an airport. Next to the coffee cup lies a pile of colorful stickers showcasing 3D renderings of CT scans

En route to the Twin Cities MN for #JMIH2025 ✈️ I'm bringing plenty of stickers for y'all so you have an excuse to hit me up and talk fish and herps 🐟🐢🐠🐡🐸🦎🐍🐊

Catch my talk in the #ASIHin3D symposium on Saturday...

I made these, they haven't been used for teaching yet though: bsky.app/profile/jaim...

You can buy models like this online, but they are pricey (100s of $ each or >$1000 a set). I made these using NSF funded *free* data (from the oVert project), a few bucks worth of PLA filament, and sandpaper & paint (a combo of automotive and acrylics).

Top: black and white 3D rendering of a dusky basslet fish Bottom left: purple/pink 3D rendering of the brain of the fish, with a scale bar representing 0.5 mm Bottom right: A photograph of a 3D printed and painted anatomical model of the fish brain on a white stand, with colors demonstrating anatomical regions.

Top: black and white 3D rendering of a midwife toad Bottom left: purple/pink 3D rendering of the brain of the frog, with a scale bar representing 1 mm Bottom right: A photograph of a 3D printed and painted anatomical model of the frog brain on a white stand, with colors demonstrating anatomical regions.

Top: black and white 3D rendering of a plated lizard Bottom left: purple/pink 3D rendering of the brain of the lizard, with a scale bar representing 3 mm Bottom right: A photograph of a 3D printed and painted anatomical model of the lizard brain on a white stand, with colors demonstrating anatomical regions.

I used my 3D printer to create educational anatomical models of the brains of fish, frog, & lizard 🐟🐸🦎 The (color-blind friendly) colors demonstrate anatomical regions, and the 🧠 are many times larger than their real size. They can be removed from their stands for closer examination/comparison 🧪

Seven 3D renderings of caecilians (limbless amphibians) arranged on a balck background. Each is rendered in a different color, from left to right and top to bottom: red, teal, electric blue, purple, green, orange, yellow.

Who are those sweet slippery noodles with tiny eyes? Caecilians of course! 🥰 I imaged these limbless amphibs for #oVertTCN using #diceCT to enhance the contrast of the soft tissues. You can find the datasets on MorphoSource with the other diceCT amphibians: www.morphosource.org/projects/000... 🧪

This gopher tortoise also features in my 2023 diceCT turtle paper: doi.org/10.1002/ar.2...

I used this specimen to create the world's first ever whole body diceCT turtle dataset!

Screenshot of the media page on MorphSource, showing specimen/media details on the left, and 3D viewer with controls on the right. A colored 3D model of a gopher tortoise skeleton is shown in the 3D viewer.

I also urge you to check out the re-vamped MorphoSource online 3D viewer! The team has been working on new features for it, including the ability to save annotations, take measurements, new navigation controls, & camera settings. You may not even need to download models to collect data you need!

image with black background, showing a colored 3D model of a gopher tortoise with bisected shell and transparent right side, revealing the skeleton inside. Shown in anterior (top), anterolateral (middle), and right lateral (bottom) views. An image of the museum specimen on a white background, with scale bar, is shown in the top left corner.

Can we just take a moment to appreciate turtle skeletons? 🐢🦴🤯 The original model of this gopher tortoise skeleton on Sketchfab (skfb.ly/ooVZS) is a crowd favorite & I've received requests for a downloadable version lately, so I uploaded a new one to MorphoSource: www.morphosource.org/concern/medi...

Done by hand, mostly with a thresholded 3D brush. No scripts! This one was segmented in 3D Slicer, and further mesh editing (clean up, simplification, colors) done in Blender.

Glad to see Vera et al. lead the way for 3D data sharing in Aus. I hope that Ozboneviz 🦴 shows great things that can happen when you share 3D data FAIR-ly. After working on oVert & seeing it be an amazing thing for US collections, it's somewhat poetic that this paper comes from my home state of SA 🥰

The result of three years’ worth of travel through Australia’s museum collections and three Universities, and heaps of help from the MorphoSource and oVert Teams @jaimiagray.bsky.social :

New Colorize Volume module Just added to 3D Slicer 5.5 is the new Colorize Volume module! I tried it on a fully segmented rattlesnake skull with really nice results comparable to the expensive proprietary software VGStudio Max....

Hello I would like to add that Slicer just keeps getting better - new modules are being written all the time. My fave is the Colorize Volume module they whipped up a couple years ago after I demo'ed the layer-style rendering in another (very expensive) software

discourse.slicer.org/t/new-colori...

All scans for this specimen were funded by NSF and #oVertTCN, and are available on MorphoSource, including contrast enhanced #diceCT scans! If you look closely, you can see that I had to digitally re-attach its tail to make the rendering ❤️‍🩹

www.morphosource.org/concern/biol...

On the left of the image are three different views of a 3D model of the skull of a leaf tail gecko (Phyllurus platurus), with all bones isolated and colored to demonstrate skull anatomy, from top to bottom, anterolateral view, dorsal view, and anterior view. On the right side of the image is a 3D rendering of a contrast enhanced CT scan of the whole body of the specimen, rendered in purple.

Decided there's not enough lizards in the #ColorsOfSkullAnatomy collection 🦎 So, new to the gang: Phyllurus platurus (southern leaf tail gecko). An Aussie lizard of course, and one of the 1st specimens I scanned at Florida Museum in 2021
www.graysvertebrateanatomy.com/leaftail-gecko-skull-anatomy/

The computer lab at UTCT, with large monitors showing CT data being processed by students. Dave Edey sits at a PC at the front of the room, demonstrating how to use the Dragonfly CT processing software.

Had a marvelous time teaching our UTCT bio/paleo short course this week! 3D Slicer and dragonfly, with a hint of Blender and diceCT... Participants are now equipped to go forth and render/segment/measure/analyze their CT data 🤓

Sign that reads "welcome to UTCT bio/paleo short course, Jessie, Dave Romy, Jaimi"

Today we welcome our bio/paleo short course participants to UTCT! Three days of CT and data processing, coming right up 💁

The Non-Clinical Tomography Users Research Network standing all together in the dinosaur hall at the American Museum of Natural History

And that's a wrap on our NoCTURN 2025 meeting at the @amnh.org 🎉🎉 I'm brimming with pride at all the things we've been able to achieve! Just the most marvelous community (who knows how to have a good time). Look at all the things we did (much more still to come 😉): nocturnetwork.org

ToScA attendees were living it UP on our dinner cruise in New York city 🗽🛥️

Jaimi Gray presenting on stage behind a podium at the American Museum of Natural History. The slide behind her details the number of genera the oVert project scanned.

Got to stand up at the @amnh.org & tell everyone at ToScA about the #oVertTCN project and some of the fun things it led to...
🐒🦌🐀🦜🐸🦎🐊🐢🐦‍⬛🐟🐍🦔

I had a blast yesterday teaching Slicer in this funky dome at @amnh.org! Thanks to all the attendees for coming along for the ride 🎢🧪