Golden Lion Tamarin: a study in light and color

I started this illustration as a from a sketchbook sketch to practice color and light, and fur techniques. I believe that as a result of the initial painting phase being fast, this illustration has a more painterly style than I normally achieve, though I’m pleased with the texture. I plan on doing more small illustrations like this one in the future to explore color, composition, movement, story, etc.

goldenLionTamarin_web

sketch_web

Chrysochloris Anatomy Reference

About the scan
    This CT scan was provided to the Luo Lab by the folks at Digimorph, located at the University of Texas Austin. Many thanks to them and their public database. Chrysochloris (golden mole) has pronounced digging adaptations, such as broad but short hands, powerful forelimbs (note the large lever arm created by the olecranon process and large scapula), and a shovel-like snout. The original information about this scan can be found here. These images were created using the segmentation software Mimics.
Why I’m sharing
    I’m sharing this because I have found it very useful, both from an artistic and an anatomical point of view. I find it particularly interesting to see how the muscle mass sits on the bone, particularly around the snout. It is also good to note the volume of hair and skin. I hope others can find these following images useful.
ant_01 lat_04 lat_03 lat_02 lat_01 ant_04 dors_02 dors_01 ant_03 ant_02

Workflow Part 1: CT scan to 3D model

Our lab bought a MakerBot Replicator2 a couple months back. I was super excited about using it, and still am excited about maker technology, but quickly realized that this was not like a regular printer; you could not simply take it out of the box, plug it in and expect it to work. It has been a steep learning curve getting it to cooperate and I think I’m getting closer to having a more consistent success rate with the prints. Since taking charge of the printer, I have walked a couple of people through the process of creating a 3D print from a CT scan, which is what has inspired this series of posts. Hopefully someone finds these helpful for their own endeavors.

Part1: CT scan to 3D model

Fossils are usually scanned using an industrial scanner that can pump a higher than medically allowed dose of radiation into the specimen. Denser materials need a higher amount of radiation to penetrate them and, obviously, fossils are far more dense than flesh and bone. If it is a micro CT scanner (microtomography), the resulting images can also have a great deal more resolution that a typical medical scanner.

IMG_0423

A fossil sits on the rotating table in front of the X-ray tube.

After the fossil has been scanned, the outcome is usually a stack of .tiff or .jpg files. A medical scanner would produce a DICOM file. The difference is this: a DICOM file comes with metadata that describes the voxel size and orientation of the scan, whereas for a .tiff stack, the voxel size and orientation needs to be entered manually. A voxel is a three dimensional pixel. To produce an accurate model, you need to know the exact dimensions of the voxels, otherwise the models may be squished or stretched. The X and Y  voxel size (which should always be the same) can also be calculated by dividing the field of view (aka the size represented by the width) by the number of pixels in that width.

There are several programs you can use once you have obtained the dataset to extract the information (aka make a 3D model from it). The more common ones I have encountered are Mimics, Amira, Avizo, Osirix, and VG Studio. The bulk of my experience is with Mimics, as this is what we use in the lab. However, Mimics is a professional piece of software and likely out of the budget for a casual user. If you happen to be extracting CT data for your own use and use a Mac, I recommend Osirix, which has a free license. By the way, if you have ever had a CT scan done of yourself, you have the right to ask for that data from your doctor, but make sure you ask for the DICOM dataset. You can also request that your patient information is removed from the file that you receive, for privacy purposes. This is just one situation that the casual user might find the need for Osirix.

Next you need to section out the relevant geometry. This process obviously differs between software, but all are based on selecting a portion of data based on the density of the sample. This can be tough if the fossil and matrix have similar densities. Samples that contain metallic elements can also be problematic. These high density irregularities can cause flaring and makes it difficult to get a wide range of grays (as is desirable) for the fossil and matrix. In effect, this throws an outlying cluster of high density that tips the histogram in that direction.

Once you have your model sectioned out, it gets exported as an .stl file. In the next post, I will discuss how to clean and process the .stl file for 3D printing.

Click here for Part 2: preparing a model for 3D printing 

Life after BVIS: a new chapter

I created this blog early in my studies at UIC to track my progress through BVIS. I have now graduated and cheerfully entered a new phase of my life. Now I must ask myself what should this blog become. Perhaps it will be a medium to share interesting and insightful art and science as well as a place to showcase my own work. More on that later.

Now on to what my life has become as a BVIS graduate. I have had the extremely good fortune of being offered the position of Scientific Illustrator for Dr. Zhe-Xi Luo’s lab at the University of Chicago. I became familiar with Luo’s work while working on my research project about multituberculate forelimb movement. Luo’s work focuses on mesozoic mammals. You can see the lab’s mission statement here. The work I will be doing for him includes illustrations (mostly digital) and using programs such as Mimics to extract CT scanned specimens. I would like to note, however, that I am still open for commissioned work, as this position is only considered part-time. Please do contact me with inquiries for commissioned work.

As awesome and fulfilling as the work is, it may be some time before I can share any of my work from the Luo lab here. I will not be posting illustrations before they are officially published, but when I do, I plan to talk a bit about the science and decisions behind the illustrations too. In the meantime, I hope to continue doing art for personal growth, and that I will be able to share here.

In conclusion, life is good. I have emerged from BVIS with a fantastic job filled with potential.

Until next time…

Final Animations from Spring 2012

So, spring semester of 2012 is over, summer is on its way, and I have several animations to post to bring this blog up to date. I took two animation classes this past semester, a Maya class that focused on dynamics, and general animation class that focused on adding to and cleaning up my portfolio and creating a demo reel.

I’ve mentioned my flower animation before. It’s filled with nCloth, even though it’s subtle in some places. It opens with a realistic scene, where I used mostly architectural textures and environmental lighting from an hdri map. The rest of the animation I wanted to be more stylized and look a bit like an illustration. I got the flower textures from dissecting a sorbonne lily and scanning the parts. Fun fact, flower cross-sections look really cool:

… And here is the finished project:

 

And lastly, here is my final demo reel. I don’t have too much to say about it, since I’ve mentioned most of the pieces before here on my blog.

 

The question I’ve been most confronted with lately is, “What are your plans for summer?” I delayed graduating this month to give myself the summer to complete my research project, which I hope to be finished with by mid July. This will be taking up the bulk of my time, but I certainly have a bunch of other projects I want to touch on. Some of the other projects I have set for myself is to create a mobile friendly version of my website, learn ZBrush, and play some more with dynamics and MEL scripting in Maya. And then there are the piping competitions (yes, I have been playing bagpipes since I was about 11) that also take up quite a bit of time. So, in conclusion, I have a busy summer set for myself, but at least it’s filled with a bunch of fun things! Oh, and I forgot to mention job hunting. That’s important too.

Anatomy of a Retrovirus

My most recently finished animation is a basic introduction to the anatomy of a retrovirus. The animation is meant to be appropriate for an intro-level biology course. The capsid and reverse transcriptase models were imported from the Protein Data Bank and it was animated using 3ds Max and edited in After Effects. Enjoy!

Research Photo Journal

Over the last couple of weeks I have accumulated a bunch of pictures from my research at the field museum, so I thought I’d share some.

articulated skeleton of Hemicentetes nigriceps (aka Highland Streaked Tenrec)

Skins for Hemicentetes nigriceps

A drawer full of solenodons

Echinops telfairi (Lesser Hedgehog Tenrec) seems to be a close match

Playing with clavicle articulation of Tolypeutes matacus (Southern Three-banded Armadillo)

I was quite surprised to come across this Priodontes maximus (Giant Armadillo), which was about the size of a toddler!