Jason Freeny

When people think of "anatomy" a few key species come to mind - humans, of course, and then our favorite pets (cats, dogs, horses, snakes, etc.). Some people may start branching out into the less domesticated animals, like deer or sharks or birds. However, Jason Freeny has decided to chart out the anatomy of previously overlooked subsets.

Like gummy bears.



Created in 3D and very well thought out, these prints of the anatomical charts for various objects we see in our lives (lego-men, balloon animals, Domo-kun, and the previously mentioned gummy bears to point to a few) are fantastic. High quality, amusing, and with the added advantage of being very convincing. Jason also has a facebook page where he sometimes posts updates of projects as they are being made, which is always a treat.

not always just posters - his work is available in various formats

Domo-kun

a close up of Domo-kun as he was being made

UNITE Conference

So, I've been fairly remiss in not talking about this wonderful program known as Unity3D. A 'step up' from Papervision3D in that in actually handles 3D meshes rather than a Flash mock-up of 3D, Unity3D is a comparatively inexpensive game engine used by both indie designers and larger companies. The editor runs on both the Mac (OSX) and Windows platforms, thankfully. It also outputs games for multiple platforms - a Windows exe, a Mac program or widget, Wii game, iPhone application (actually a separate Unity3D engine designed specifically for iPhone development), and web-based browser games that run off of a plugin (supported by both Mac and Windows).

I've personally done a small amount of work in Unity3D (and hopefully will get more done... but work has me extremely busy so we'll see). If you know JavaScript, beginning to program within Unity seems to be fairly simple. It also accepts Boo, and C#. The JavaScript is slightly different than the JavaScript used on the web - I liken it to the difference between American English and British English. There are also tutorials by Ethical Games for the change over between Flash and Unity3D. In any case... it's a great program to work, at least in my personal experience.



There is also a conference coming up, in San Fransisco, called the UNITE 09 Conference. Being in San Fran this year, and since I recently moved out to the West Coast, I am super excited about it. I plan on catching at least a couple of days, if not the whole conference. As I said... busy with work, unfortunately. The Agenda looks great - everything from an intro to Unity3D, to Unity for Flash Developers, to a Post Mortem look at some games, shader analysis... I'm very excited, to say the least. More once the conference actually starts!

Gaming and Training

While visualizing CT and MRI scans as 3D colorized volumetric images is not a new thing (see OsiriX, Fovia, VolumeGraphics, Amira, Mimics, 3D Slicer and many others that I personally don't know about), it is becoming quite popular for training and surgical planning. However, BodyViz actually uses an X-Box controller to bring the 3D patient scan to the surgeon. Personally, I find the use of a video game controller to be highly intriguing. As my generation grows and becomes the doctors and surgeons of the future, I know that I would prefer them to look at my body first before preforming surgery. And coming from a gaming background, using a game controller to move through a data set makes a certain amount of sense. Whether it be on this technology or something similar, I find the possibilities growing, and very exciting.

Video Game Technology Helps Train Surgeons

From BodyViz:

BodyViz has extensive visualization features that enable users to quickly and effectively view and interact with their patient's data in a never-before-seen 3D manner that is changing the way medical professionals view their world. The user interface is operated by an Xbox 360 controller which allows anyone from surgeons to medical/anatomy students to simply “travel” under the skin, past the bones, through the arteries, blood vessels and organs and literally fly through patients’ bodies. The game controller lets physicians create "clipping” planes and insert virtual surgical tools that can be maneuvered around internal structures of the anatomy in all directions. Users can also choose what tissue densities to view and from a variety of colors to enhance the data. BodyViz is affordably priced, lightweight and simple to use on laptops or PCs.

3D on the Brain

So, some of us have 3D on the brain. However, some of us construct interactive 3D models of the brain. Well... at least the cranial nerves. Created by a talented 3D artist, Kieran Meek, and vetted by doctors to ensure accuracy, the eHuman Cranial Nerves iPhone app rocks. (And I'm not just saying that because I work there...) In any case, I believe that this app can speak for itself.

"Learning the 12 cranial nerves and the foramen in the base of the skull are an essential component of every anatomy course; all health professionals, anatomists, biology students and anthropologists have had to memorize their names and functions. Our app allows students to enjoy learning the nerves and foramen in a highly visual, interactive environment. The models are reconstructed from a high resolution CT scan, and the user can control the position and transparency of the skull and each nerve. Accompanying textual information is just a tap away."

Solid view

Semi-Transparent view

As stated in the image... Selection Mode


And an example of the information pages

If you have $5 to spare (and an iPhone or iPod Touch) you should pick it up just based on pure 3D awesomeness. Even if you don't have the $5, bring lunch from home one day and buy the app instead :).

(although this post may just be proof I shouldn't update at 1am. I know the bad pun at the top is...)

Museum Update

Well, I am still beyond tickled to see work I've done in OsiriX being used by the Fine Arts Museums of San Francisco. Short explanation of how the images were made to follow.

So, because I feel like sharing, here are two of the flyers in which my images are used. (the flyers are the work of the design team at the Museum, I just provided content).

The Press Release flyer.

A promotional flyer, first page.

First of all, I must admit that I have upgraded the computer that these images were made on to 64 bit version of OsiriX. It is an 8 core Mac Pro, with at least 4 gigs of memory, perhaps more. I drool over it, but it's not mine. In any case, it handles large case files well- and this was a very large file. Multiple scan inputs, with the largest being over 4,000 slices. Needless to say, the 32-bit OsiriX, while open-source and awesome, could not handle this dataset.

So, by upgrading to the 64-bit version, we were able to utilize the full power of the machine. And let me tell you, for 3D visualization purposes, I highly recommend the upgrade. It's amazing and well worth the money. And doesn't it just give you a warm fuzzy feeling to know you are supporting a favorite program? Maybe that's just me... If the warm fuzzies don't do it for you, knowing that a 3000+ data set can be opened without hiccups and in less than 2 minutes may peak your interest. I am thoroughly enjoying the upgrade, when I get to use it.

Now that the program handles the dataset (barely), it takes hours of fine tuning to get any sort of recognizable image. I much prefer working with live humans, as the cadavers (especially mummies!) just don't have the same clarity. None of the pre-set CLUTs that come with OsiriX truly worked with this mummy data, but I had a very interesting time coming up with my own 16-bit CLUTs to use and save. The results were quite interesting, and for the most part, the museum didn't ask for any major changes. I did tweak the overall color in Photoshop (from a red to a golden-orange), but no cover-ups or major Photoshop changes.

I do love OsiriX and any opportunity to use it is great fun, not just work.

That is pretty much it. Now, I have to find someone I can vivisect to see the brachioplexus in action. Any volunteers?

Meet the new "Working Me"

Soooo... with the advent of my internship and then subsequent job at eHuman, I have been beyond busy. I don't think they've invented a word that actually covers how much work I'm doing. Which I am not allowed to post. There's this whole 'non-disclosure' agreement companies make you sign...

In any case, I can post things that have been released into the wild, so to speak. So, here are some images I generated in OsiriX for a mummy that was recently scanned at Stanford. Some are !gasp! actually being used in print. (which I am actually incredibly giddy about...)

The Fine Arts Museums of San Francisco are putting on the Very Postmortem: Mummies and Medicine exhibit.

"Archaeology meets technology in this small-scale exhibition exploring the scientific examination of mummies and providing new insights into the conditions under which the Egyptians lived. Included is the sarcophagus and mummy of Irethorrou, a priest from Egypt around 500 B.C. His mummy has undergone a CT-scan that allows a unique viewing experience of a three-dimensional “fly through” of the body and a forensic reconstruction of his head."

Here are some images from their flicker archive of the transport of the mummy.

Being scanned by a 'c-arm' scanner at the Stanford Hospital.

Checking out the incoming images.

Meeting Irethorrou close up. He was a priest in Egypt from about 500 B.C.

And now, to meet him internally as well.... Here is a sampling of the OsiriX images that I generated.

A full body request - although the arms were not attached to this version of the scan. Because of the size, the mummy was scanned in multiple parts and then stitched together by the wonderful Robert at the eHuman office.

This image (without the logo and turned completely vertical) was used in the promotional flyer for the exhibit.

This was another one specifically requested to show this amulet. It has been decided that it is the "Eye of Ra" and they wanted to showcase it. Unfortunately, OsiriX may not be the best program for that. No matter how much I tweaked, that was the highest level of detail that came through on the amulet in OrisiX. So I doubt they will be using this one.

I am very excited to see the exhibit all put together, and can't wait for the 31st! (Opening it on Halloween is cute, I swear).

I will also attempt to post more often. Hopefully some other projects will become 'public friendly' and I'll be posting about other projects that eHuman is producing. It's an exciting time to be here, and I am absolutely loving my new job. And the fact that I have a job. Now this whole 'must graduate' thing is another story...

Atlantis

Well, it's been quite a while. I'll start catching up on what I've been doing this past month over the next couple of weeks or so. One of the things I've been working on is an update to the submersible scene that I've posted here before. I've updated some texturing, played with a few new camera angles, and put in some more dramatic lighting. Obviously, I'm not finished with it yet. Any comments or suggestions that you have, I would love to hear.

Just to re-iterate. The sub was originally built in 3Ds Max 2008 as part of a challenge I was unable to complete. I took it into Maya this semester to spiffy it up and add it into an animation. The scenes are rendered with Maya software when I could get away with it, Mental Ray for the first two scenes. Personally, I think it shows and I can't wait to actually have the time to let my computer render it out.




This was all keyed by hand rather than using any sort of dynamics system. I may change that in order to get a little bit more natural movement in the beginning. Animating the chain holding the sub up is proving to be a pain. I hope I can rig a hair system that will flow a bit better. I've done it before, but it's been a few years. I also need to add more animation and character to the last scene where we are following the sub. Not to mention that is an awfully barren sea floor, and those ruins are kinda pathetic. I have plans to continue to build that environment up so it is much richer.

I'll continue posting more on the animation front after I move across the country. Egads.

Atherosclerosis - Blood Vessel

Here is one of the latest things I have been working on - Atherosclerosis. This takes place in one of the coronary vessels of the heart. I would consider this a "second stage" animatic, as the first stage was something I was ashamed to post even here.

In any case, this was done in Maya. I used a basic particle system for the blood, with a rotating erythrocyte instanced onto the particles - with a uniform field, a turbulence field, and a radial field also affecting the particles. They still have some self collision issues that need to be worked out, obviously. I attempted to use the work around of having each particle generate a radial field, but while that partially works... it also causes the blood to be very jumpy in parts.

I also feel that the turbulence field may be turned up too high, and the rotation of each individual erythrocyte needs to be slowed down a bit. I had to use a trap function of the turbulence to stop the particles from intersecting with the blood vessel wall, despite the "make collide" feature being activated. The GeoConnectors may have some issues associated with them right now that require further research.

The vessel distorts with the use of a blend shape. Obviously, this is not the final texture. However, it did show me that the texture may stretch when I apply it to the vessel wall. I'm wondering if a texture morph may work better, if Maya even does that. I know 3DsMax does, but I haven't tried it in Maya yet.

The background was just a quick fill so it wasn't just floating in space. It was added in AfterEffects without a lot of tweaking, so it doesn't quite match the camera. When the final animation is finished, the actual heart will be composited into the background with the correct camera moves. White blood cells and platelets will also be added, hopefully with a 'liquidy' effect as well. I plan on doing some research to ensure the scale is correct between the vessel wall and the blood elements, as it is a coronary vessel and a bit smaller than say.. the aorta.

I would appreciate any thoughts or comments as I work this video out.

Volcano

As promised, a volcano. Also done for a class tutorial project in Maya. I slapped a water-like plane and a sky sphere into the scene to give it a slightly more natural look. I also did not include sparks coming out of the volcano. Sparks are rendered with Maya Hardware, seeing as they are streaks, not sprites or clouds.

So, there is a sprite volume emitter spewing smoke (way too fast, by the way, but I didn't feel like tweaking the uniform field on it any longer). The volcano was made live, a curve drawn on the surface, and then it was made into a flow emitter with blobbies. Finally, there is a second volume emitter with cloud particles for the steam.

I found that working with particle systems is a heck of a lot of tweaking and fiddling, but it can be fun. Especially if you have a book nearby that you can read while it is rendering.

So, a volcano, in the middle of the ocean with nothing else around, on a bright sunny day.... 3D, maybe? Naw...

"Ring of Fire"

So... wow, school sure is busy. In any case, here is a quick tutorial that I worked on for one of my classes. It's a semi-homage to my program, Biomedical Visualization - or BVIS for short, in case you can't tell. I didn't want to just have an animating circle, which is what the tutorial called for. And when I say short, I mean it took me about 20 minutes, and that was only because I had to retrace part of my steps for the texturing.

This was just a quick "emit from curve" with a scale animation on it. The fire texture was yanked from a procedural texture from Maya. I did have some issues with density, but I just ended up copying the sequence in After Effects rather than try to render it out to tweak it.

There was a volcano tutorial that was a pair with this one, but I am having severe issues with the curve actually adhering to a live surface. It's driving me nuts, really. So, no volcano.

Now, I'm off to do something (hopefully) productive and related to the multitude of projects that are looming.