Revealed

A blog about scientific and medical visualization and all that’s involved.

Archive for the ‘digital 2D/3D’ Category

Agents of Deterioration Interactive Website

Posted by Janet on December 4, 2009

November marked the end of my internship at the Smithsonian. I’ve been back in Chicago for a month now but it was only a few days ago that I turned in my Master’s project proposal. The topic for my project is paper preservation for scientific illustrations, and I will be making a Flash interactive guide over the next few months based on what I’ve learned at the Smithsonian internship. Here is a very nice interactive website about the agents of deterioration–things that can harm objects, such as paper based scientific illustrations that my project focuses on: http://www.liverpoolmuseums.org.uk/nof/agents/

Posted in digital 2D/3D, Smithsonian internship | Tagged: , | 2 Comments »

3D Lamp Contest Poll

Posted by Janet on September 18, 2009

Here is the lamp shade I designed for the 3D Print Lamp Contest hosted by i.materialize for Blender artists:

cchao1-GFP-LampHope this appeals to the science illustrators and anyone else who’s likes proteins, jellyfish, or anything that lights up 😉 Please correct me if you catch any mistakes, it was getting late…

To vote for your favorite lamp design (and please do, the top 3 winners get their design fabricated and delivered), follow these steps:

1. View all the designs here.

2. Register with the Blender Artists Forum at http://blenderartists.org/forum/register.php if you haven’t already. Sign in.

3. Vote for your favorite design here. Only one design per voter.

Posted in announcements, digital 2D/3D, my projects | Tagged: , , | 3 Comments »

Print Your Own Lamp!

Posted by Janet on September 12, 2009

I will be blogging less frequently for the next few months. I’m trying to graduate by December so project research needs to come first, and time is running out…

That said, I’ve been teaching myself Blender over the past couple of weeks and just came across this 3D printing contest for Blender artists. The contest is sponsored by i.materialise, a 3D printing business. The rules for entering are simple:
1) Register with blenderartist.org forum
2) Design your own lampshade using Blender, following the guidelines here http://i.materialise.com/blender (click “Download Plugins” on the left hand column, then download the pdf followed by the appropriate files)
3) Post 3 screenshots via Reply here http://blenderartists.org/forum/showthread.php?p=1462901#post1462901

The rules are explained in detail in the above link too. The top three winning designs will be printed and delivered to the winners for free.

The deadline for the submission is Wednesday Sept. 19. Not a lot of time, I know. I wish I had found this sooner too but I’m going to give it a shot anyway. How many other chances do you have to have your own lamp design 3D printed for free?

Posted in announcements, digital 2D/3D, Uncategorized | Tagged: , , | 1 Comment »

Modeling Lung Anatomy

Posted by Janet on August 8, 2009

*3ds Max lung model © Denoyer-Geppert, images used with permission.

Following “Visualizing Lung Anatomy,” I can now begin to model the lung. First, I took screen shots of the lung in VolView in three orthographic views–top, left, and front. Then I set up three orthographic planes and added each image as materials to the planes. I prefer this method over using a background image because this allows you to see the images in perspective views as you rotate objects. You also don’t have to worry about shifting your objects and locking zoom, which in my version of 3ds Max gets a little quirky.

LungModel1

Next, I put more planes in the scene, took a screen shot of every twentieth slice from the data set, and applied the screen shots to the planes as materials. Now that I have slices of the lung from front to back, I outlined each slice in the front viewport. Notice that the outlines are all located on the same plane. This will be fixed later. (If you are wondering why the “right” lung is on the left side, it’s because the “person” is facing us so their right is our left.)

LungModel2LungModel3LungModel4

Once the outlines are complete, I calculated the distance I must offset each line in order for it to fit the profiles correctly. After the outlines are moved to their correct positions, you can clearly see the shape of a lung in the perspective view. The lines must be linked together in order for a surface to be created. I selected one outline and used the “Attach Multiple” option under the modify panel. For now, I keep the front and back halves separate so I can easily hide the back side when necessary. Then, using the “Connect” and “Refine” features under the modify panel, I connected vertices between the outlines.

LungModel5

Here is what the model looks like with connections between the outlines:

LungModel6

Using the “Surface” modifier, I created a surface using this mesh. At this point it’s not perfect. I must go back and adjust the mesh until the entire surface can be covered:

LungModel7

A model of the lung without holes in the model:

LungModel8

The lung is looking nearly perfect, but overall still appears rough. Adding “Relax” and “TurboSmooth” modifiers will help refine the mesh:

LungModel9

This is one way to make a model of the human lung. I chose this method because I wanted to capture the accuracy in shape and had tools to visualize CT scan data. I also chose not to model the lobes separately because they are not the primary concern for this project and can be added later using materials.

Posted in anatomy, digital 2D/3D, my projects, techniques | Tagged: , , , , | 2 Comments »

Visualizing Lung Anatomy

Posted by Janet on July 27, 2009

One of the projects I’m currently working on at home involves building a 3D model of the right lung. To make sure the model will be as accurate as possible in terms of shape, I would need to know the lung anatomy before I begin building the model.

The first thing I did was going to a library to look at drawings and photographs of lungs. I did a few quick sketches and wrote down some notes on how I will approach this in a 3D program:

sketch1sketch2
Now comes the fun part…

Next, I went to CVS and bought some Crayola modeling clay and began to build a small lung model while looking at online images of the lung. I tried to find as many variations in as many angles as possible, but most resources only showed the standard views. The e-anatomy website very helpful for this initial step, since it provides cross sectional images, labels of structures, and several different ways of presenting the structures. (The website is free, but registration is required to gain full access to the labels and features. High res images and full screen mode are available with a fee, but for our purpose this isn’t necessary.)

The purpose of making a clay model is to get a concrete physical sense of the three-dimensional shape. I find this step very important because it forces you to piece together two-dimensional visuals into a three-dimensional object. It is through this process that I begin to realize the complexity of the shape of a lung.

Below: Clay lung, heart, and a piece of unused clay.

clay-lung

To begin the digital visualization process, I looked further to find visualization tools that would allow me to use actual human data, look at the structures from various angles, and isolate unnecessary structures. Osirix, an open source DICOM viewer, is perfect for the job. It even has data sets available for download. The only problem is…Osirix is Macs only, and I only have access to PCs.

After poking around for a while, I found a similar product called VolView that works on a PC. VolView comes with a $1000 yearly or a $2500 unlimited licencing fee, but it has a 30 day free trial for download. I was able to import a data set from the Osirix website into VolView. My impression of VolView after two days is that it is very easy to navigate, comes with instructions (Help –> Help Topics), gives good results, and has powerful features. One thing I haven’t figured out is whether there is a cut feather that allows the user to trim away unnecessary parts. There seems to be a segmentation tool under the “Analysis” tab, but the instructions for this feature is limited and it is a feature that does not allow “undo.” That is scary. The first time I tried it, it messed up a model I had been playing with for two hours, but it warns you first so you feel like it’s your own fault for not listening. Luckily I was able to reproduce the same result ten minutes later. Here is a screen shot of my lung visualization:

volview-lung
…and a detailed shot of the lung. You can see the bronchi entering the right lung, but notice there are still some artifacts on the side.
volview-lung-detail

*See “Modeling Lung Anatomy” for the next step in this process.

Posted in anatomy, digital 2D/3D, my projects, photography/imaging, techniques | Tagged: , , , , | 4 Comments »

Interview with Jim Hoerricks

Posted by Janet on April 22, 2009

While working on a project, my internet search took me to a blog called “Forensic Photoshop.” Being a long time fan of forensics and a user of Photoshop, I was curious to find out more about the author behind this blog. It turned out to be Jim Hoerricks, a forensic image/video analyst who not only writes a blog, but is also the author of a book by the same name. I contacted Mr. Hoerricks two weeks ago and he immediately agreed to an e-mail interview.

forensicphotoshopbook1

me: “First, could you tell me a little about you and what you do with the LAPD? Is this something you’ve always wanted to do?”

Jim Hoerricks: I’ve always been into art, the process of creation, crafting, designing, and so forth. I started out as an artist/designer. My first gallery showing and sale was in the 8th grade (some valuable lessons in contracting were learned there). I started out with art as a business in my shared flat in college, doing flyers for parties and so forth. I got a graphics job on campus that later lead to the editor’s job with the college’s daily newsletter.

Over time, I built up a client base. My primary function, my position with my clients, is to find out what they need and deliver it on-time and at a value that they and I can both afford. I’ve done everything from menu boards, to ad sheets, to Excel applications. Later on, with the advent of things like Microsoft Publisher, clients brought their art departments in house to save money. Some came back after a while. I still maintain a small list of clients whose accounts are more like personal relationships than business.

In 2001, I was offered the chance to join the LAPD as a civilian specialist and start the Forensic Image/Video Analysis lab. It took a few years of chasing down funding and equipment, writing SOPs, and whatnot, but I eventually got it all going.

To answer the “is this something that you’ve always wanted to do” question, I’d have to say no … inasmuch as the job, the technology didn’t exist to exploit images the way that we analysts do until I was already in college. Even then, I wasn’t aware of what was happening in the industry. I simply love to create, love the challenge of crafting something new. There’s a lot of technical cross-over between my background and this new industry … so it just fit. It just made sense. I could edit on an Avid, on Premiere, and Vegas … and these are the primary tools for a forensic analyst. Then there’s Photoshop. Everyone uses Photoshop, which is my real strong point. Then I can bring in all of the other software and hardware tools … and the Workflow was born.

me: “I’m sure when many people hear about your job, the first thing they want to know is “how close does it resemble forensic TV dramas such as CSI and NCIS.” Is your job as exciting as what we see on TV?”

Jim Hoerricks:
There is no “CSI” button, obviously. 🙂 The question is valid, and there is a “CSI Effect,” but I think of it in terms of another challenge. Instead of sitting by bemoaning the fact that these shows exist and people watch them, I look to them for research into what juries expect. If a jury expects to see a face resolved from a reflection in a nearby window, and I can resolve the image … great. If not, I can tell the story, my testimony, as if I was within that “CSI” episode. “In CSI, the latent prints are lifted from the whole car in a matter of minutes. Fade to black, off to commercial, and when you return, there’s a match … the reality is much different.” Then I explain why.

Is the job as exciting as TV? No. An unfortunate “side effect” of the work is vicarious trauma, the trauma that your brain endures as you watch (helplessly) as bad things happen to real people, over and over again. In one murder case, I watched the footage over 500 times during the course of my work. It has an adverse effect on your mental health. The trauma can lead to things like depression and PTSD if not recongnized and mitigated. Thankfully, I’ve got a former client who’s an expert in this area. He’s helped tremendously.

I don’t think people realize that there is a psychological difference between watching Arnold blow up a town on TV (then seeing him as Governor later in the day) and stepping around an actual dead body or watching someone actually get hurt on video. Remember the Faces of Death videos from the 80’s? Remember the public’s reaction? There is a difference.

(comment: I couldn’t agree more that there is definitely a greater distinction between the real work and TV drama than many people might realize. It makes me cringe whenever an illustrator delivers facial reconstruction in minutes, and *computers* magically reconstructs accidents without much input on the part of the visual specialist. I think sometimes it is difficult for people to grasp what we do because many don’t realize that sometimes the simplest images require months of preparation and research to produce. However, Mr. Hoerricks brings up a good point that TV is something that a lot of people relate to. So next time we see something impossible on TV, instead of thinking “this is impossible,” maybe we should think instead “how can we make this possible?”)

me: “What are some of the challenges you have come across in your work?”

Jim Hoerricks: The biggest challenge is staying on top of technology. As an example, every time Adobe comes out with an upgrade to the Creative Suite, it costs me a couple of thousand dollars. I’ve then got to find a way to pay for it.

People just assume that these things happen somewhere, by someone. But budgets, priorities, and finding time for things like a life and family all add up.

(comment: Indeed, equipment is expensive and it’s all a big balancing act. I was a bioengineering major before, and I didn’t realize how much more it costs to become an illustrator compared to becoming a scientist. Textbook costs are nothing compared to the Adobe Create Suite, and there appears to be such a limited source of funding for travel. I am jealous of my friends in engineering who get all their conference fees and travel expenses covered for by the school. I would love to attend every single conference that’s relevant to what I do in order to stay on top of the trend, but we simply cannot.)

me: “Can you name one thing you do that sounds fascinating but is in fact very mindless and repetitive?”

Jim Hoerricks: There’s very little that’s repetitive. Every case is unique. Different recorders, different lighting, different circumstances, different law being broken, and so forth. Having a set of procedures and a Workflow helps keep everything in order and keep me on track.

(comment: I used to draw insect anatomy every day for a year and people would ask the same thing:) No, it did not get repetitive.)

me: “You have a website, a blog, and a book called Forensic Photoshop. Are some Photoshop techniques unique to the field of forensics?”

Jim Hoerricks: They really aren’t. Photoshop wasn’t written for forensics. I’ve just taken what I know from the design/photography world and applied it to forensics. Sometimes, there are those who disagree with a particular technique, like dodging/burning for example. But it can be done in such a way that preserves the original, happens on its own layer, and does not change the content or context of the image. It can also be documented and explained to the jury … so I’m comfortable with it.

A friend at Adobe told me once that there are over 7 million “consumer” photographers and about a million professional photographers in the world. That’s a big customer base for Photoshop. There are less than 100k potential customers in “forensics” at this time. They really like us and support us as much as they can, but the art/photography world rules the day as far as Photoshop is concerned.

me:Did you ever encounter any ethical or legal issues with enhancing and manipulating images? One can argue that the more you manipulate an image, the more it deviates from the original. Does a manipulated image lose its validity in court?”

Jim Hoerricks: Words have specific meaning. It depends on what you mean by “manipulate.” Here’s how I would explain it. An underexposed image … nothing to see … all darkness. Is it useless? Not hardly. With Photoshop’s tools, I can potentially correct the exposure, adding light to the image. Did I manipulate it? Yes, of course. Did I add anything? Certainly, I added light. Did I change the content or context? No. I only added light to assist the judge and jury in ascertaining the contents of the image. Open the door to a dark room and turn on the lights. What did you do? Did the process of turning on the lights arrange the room as you see it? No. It merely increased your ability to resolve the details in the room. So you see, it all depends on how you define things.

I want to thank Jim Hoerricks again for this interview and his quick response. To view his blog and learn more about him, visit http://forensicphotoshop.blogspot.com/ and http://www.forensicphotoshopbook.com/about_me/about_me.htm.

Posted in digital 2D/3D, forensics, interviews | Leave a Comment »

Learning Flash and AdobeTV

Posted by Janet on March 27, 2009

This week is spring break. Since I’m not going anywhere, I decided to teach myself Flash.

I’ve been looking through video tutorials on the AdobeTV website, http://tv.adobe.com/. I found the Learn Flash Professional CS4 Series extremely helpful for getting myself familiar with the interface and its overall capabilities. In four days I’m able to understand how the program works, navigate with ease, create simple animations, and output a movie file. The videos are definitely worth watching. However, I will say that prior experiences in Photoshop, Illustrator, InDesign, Dreamweaver, and AfterEffects helped a lot.

The website also contains tutorials for other Adobe programs and videos for more advanced users. This is useful not only if you are trying to learn a new Adobe program, but also for learning new features in the latest version. I enjoyed watching demos of the different creative suite collections, especially in CS4 where Adobe have really begun to perfect the interface and create a more integrated workflow between programs. In my opinion, the interface prior to CS3 was extremely difficult. CS3 was a good improvement, but CS4 is the the one where they’ve nailed it (those who know me, this is the first time I’ve said anything positive about the interface. surprise, surprise). I’m sure it will improve by the next version, but I’m happy sticking with CS4 for a while.

Back to learning Flash–the one thing I felt was lacking on the internet was the amount of structured information about ActionScript for beginners. For someone like me with almost no programming skills, ActionScript is more difficult to pick up than the rest of Flash. I felt that the majority of the information was either too simple to be useful or too advanced for this skill level. At this point I think a book is the way to go.

Posted in digital 2D/3D, stores/products, techniques | Tagged: , | Leave a Comment »

Desktop 3D Scanner

Posted by Janet on February 23, 2009

Update: Regarding my comment about the object selection option below, here is a response from Ronny I. of NextEngine.

Hi Janet,
You’ve have a very interesting background. We’re constantly thinking of ways to improve our product. I’ve added your request to add the feature to trim only what is visible.
Ronny I.
NextEngine

3dscanner1

Recently I had the opportunity to try the NextEngine Desktop 3D Scanner. This is a laser scanner that scans three-dimensional objects. The data is imported into its corresponding software for editing, and the final model can be brought into other programs for further refinement.

I was surprised by how easy both the scanner and the software were to use. They actually work like they were supposed to. The scanner itself was nice because it’s small enough to fit right on your desk, and connects to your PC (sorry, PC only) via USB. It comes with a rotating platform that holds your object. My favorite part is the set up. Depending on the size of your object, the platform is placed closer or further from the scanner to allow the scanner to capture the whole object. The distance is built into the scanner settings, and by simply threading the cord that connects the stand and the scanner through different openings, the stand is automatically placed at the optimal distance. There is a part that can be attached to the platform to help hold your objects in place (not shown in the picture above). If you don’t want this part to be in the way, clay also works nicely for holding the object in place.

I was quite impressed with the software too. The last time I used a (different) 3D scanner, its corresponding software was a pain to deal with, both in function and interface. The other software had a few bugs, so I often got error messages that prevented me from continuing with my tasks. It also did not perform as well as it should. For example, I would always have trouble filling “holes” in my model–filling one hole opened up another. I haven’t had any problems with this scanner’s software, ScanStudio. The interface was easy to understand and navigation was a breeze. The performance was pretty impressive even though sometimes I do have to manually align different “shells” of the model. So far I haven’t encountered any bugs yet. My only complaint is that there is no option for selecting only the front of the object, so you have to be a little creative when making a selection. (Maybe they fixed the problem now–I’m probably using an older version)

I think the best part about this scanner is the price. At $3000, it includes the scanner, the software, other accessories, and is entirely affordable by a single person. Many scanners cost A LOT more. In my opinion, it holds up to its claim that it “outperforms many $25,000+ scanners.” Don’t worry about size either, unless you are trying to scan something very big. The fact that the scanner is small does not limit it to scan small things. Medium sized objects can be scanned in sections and then stitched together in the software.

Posted in digital 2D/3D, photography/imaging, stores/products | Tagged: , , , | 2 Comments »

Virtual Pelvic Floor

Posted by Janet on February 5, 2009

Posted in anatomy, digital 2D/3D, videos | Tagged: , , , , , , | 1 Comment »

National Geographic Best Science Images 2008

Posted by Janet on October 7, 2008

Check out the winning entries of National Geographics’ Photos: Best Science Images of 2008 here:
http://news.nationalgeographic.com/news/2008/09/photogalleries/2008-best-science-photos/index.html

Thanks Sarah for the heads up!

Posted in anatomy, biology, digital 2D/3D, photography/imaging | Tagged: , , | 1 Comment »