Revealed

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

Archive for the ‘techniques’ Category

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.

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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 »

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.

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Skin Tone Swatches

Posted by Janet on July 12, 2008

Most artists I know would agree that it is so difficult to mix the right skin tone when drawing people. Here are two techniques I came up with that may make it easier for painting skin tone digitally.

1. Grab a bunch of photos of people of different colors from the internet and use the eyedropper tool in Photoshop to take colors from their skin tone, including highlight and shadow areas. Make a swatch library and save it. Next time you need skin tones, you just have to pull up this swatch library and you’re ready to go.

Pros:
-Quick and easy.

Cons:
-Colors may look flat when you start painting large areas.

2. Dab your finger in some power foundation and rub it on medium toothed bristol board. Then do the same thing with blush and bronzers as shown below. Makeup works well because they are made to imitate and blend into skin tone.

Do this with as many shades as you like and scan it. Take it into Photoshop and adjust the colors if necessary. Using the eyedropper tool, take various colors from each swatch. Click on a few places in each swatch and you’ll get a nice range of similar colors. Save the colors in a swatch library for future use.

Pros:
-You have better control of which color you are making a swatch of, and making swatches of blush and bronzer colors will allow you to give your digital painting more depth when you layer the colors transparently on top of one another.
-You can use the same ingredients in traditional drawings to get quick skin tone effects. I’ve used it occasionally in color pencil and pastel drawings when I just don’t have the right colors. I haven’t experimented with the longevity of the materials, but they definitely work fine for small areas or if the drawing is meant to be short-lived.

Cons:
-Most people don’t have all the shades for a complete spectrum and it’s not worth buying new shades to make a swatch.

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Student Works: Kristin Luther

Posted by Janet on June 24, 2008

Kristin Luther, currently a student in the Biomedical Visualization program at UIC, explains the carpal tunnel syndrome through her illustration below. This illustration was made during her second semester in the program.

Here is what Kristin says about her work:

“We have been learning all about commonly used techniques within the field of medical illustration. The technique I used for this piece is line art made in Adobe Illustrator. I started with a scanned sketch, which I traced over (using the pen tool) and then added flat and gradient fills. The message is to explain some of the causes of carpal tunnel syndrome, and the audience is the general public.”

More of Kristin’s works can be seen on her website at www2.uic.edu/~klierl2 and Kristin can be reached at kristin.luther08@gmail.com.

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Photoshop Painting

Posted by Janet on April 3, 2008

One of the exercises I’m doing right now for “fun” is to simulate a carbon dust drawing using Photoshop. People always say there are ten different ways to do the same thing in Photoshop. Here’s how I do it.

This Max Brodel drawing is the one I plan to copy. Of course, you can also use your own drawing or simply start from scratch.
brodel.jpg

The image below is a work in progress that shows various steps I took from start to finish.
brodel-copy.jpg

-The first thing I did was place the original drawing in a Photoshop layer and traced an outline on a separate layer. Based on the outline, I made paths that outlined any hard edges in the drawing. The paths are to be used later for isolating sections in the drawing. Then I deleted the layer with the original drawing and placed another copy of the original side by side for reference.

-Then, on a brand new layer, I selected the entire outline based on a path I made earlier, and masked the area (masked area shown in pink) outside of the drawing so that the drawing stays within the outline.

-I filled this entire layer with 50% gray (see area labeled “flat fill 50% gray”) and then multiplied it with the sketch mode. Now I just have one layer with everything on it.

-Next comes the simple but time-consuming part. Keeping the brush tool at 50% gray, I painted on top of the flat fill using the multiply mode to darken, and the screen mode to lighten. By adjusting the opacity, size, and hardness of the brush, you can paint in all the details. Usually I start by using a large brush to get the overall tone, and gradually refining smaller sections. By keeping certain sections selected, you can create soft gradients next to sharp edges without interfering with the adjacent section.

-When all the main parts are done, I will use a blur tool over the entire outline and the parts between selections to avoid any unnatural sharp edges. Then I will refine the edges using the same technique above–painting with a brush in multiply or blend modes. I may also add a little noise to the entire drawing to simulate a paper texture.

I hope that’s not too confusing. By the way, it really speeds things up if you have a tablet. Until nine months ago I did all my digital work with my fingers on a 2″x3″ touch pad. It’s not impossible to paint without a tablet, but tablets make the work flow more efficient.

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Interview–Trudy Nicholson

Posted by Janet on February 14, 2008

I am absolutely thrilled to have Trudy Nicholson, one of the top scratchboard artists in the field of natural science illustration, as the first person I interview for this blog. Her name comes up over and over again when people talk about scratchboard art, so I decided to contact her and she kindly agreed to an e-mail interview.

Trudy Nicholson majored in fine arts at Columbia University and turned toward medical art school at Massachusetts General Hospital. During the thirty years she worked at the National Institute of Health, she also accepted freelance assignments in natural science illustration. Having established relationships with clients with her natural science illustrations, she continued to focus on the subject after retiring from the NIH. Here are a few examples of her works in both medical and scientific illustration.

poster.jpgsurgical.jpgsycamore.jpgcat-and-locust.jpg

Poster design, ink with overlays for color
Surgical illustration for Dr. Paul Sugarbaker, ink on scratchboard
Sycamore Annual Cycle, ink on scratchboard
Cat and Locust, graphite pencil on scratchboard

In addition to sharing her artwork, Trudy Nicholson also shared details about how she approaches her work:

me: “Did you do much self-promotion when you first started in the field? What can you recommend for people to get their names out there?
Trudy Nicholson: “When I first looked for freelance assignments I went to the Smithsonian National Museum of Natural History and talked to any curators willing to listen. This finally lead to connections and some work. Becoming a member of the Guild of Natural Science Illustrators was a great help, which continues to this day as networking within the Guild informs me and others of prospective jobs. Despite internet marketing, which wasn’t available when I started freelancing, I think that networking is an important method for finding either staff or freelance work.”

me: “What kind of references do you use when researching for your next project?
Trudy Nicholson: “To start an illustration I determine which animals and plants are to be used in what kind of setting. I get photographs of the subjects and if possible see the animals. Observing animals gives a sense of their anatomy, movements, behavior, stance and expression that photographs can’t quite give. With source material in hand I compose a very rough sketch of the whole composition concentrating on light and dark areas and keeping the emphasis on the main subject. Dark subjects or shading placed next to light areas gives contrast and drama to the scene. I gradually refine all elements until the final illustration has fine detail and the subjects are portrayed accurately. A book on scratchboard that I refer to often and that I recommend for those looking for varied approaches to the medium is Scratchboard for Illustration by Ruth Lozner, Watson-Guptill publications, 1990. The author has interviewed and included the scratchboard art of 75 illustrators giving a perspective of the many directions that artists can go using the same surface and tools.”

me: “You are best known for your scratchboard works in natural science illustration. Is scratchboard your favorite medium and why?
Trudy Nicholson: “My art has centered on animals in their habitats for publication, usually in nature related books. I work almost exclusively on white scratchboard using ink or, less often, graphite pencil. I started using scratchboard for medical work because of the ability to easily make corrections, either large or small. Gradually it has become my media preference, as I’ve become captivated by the beauty of black and white and the potential for a wide range of textures, using white and black lines and dots combined or juxtaposed in multiple ways. Since most of the books that use my illustrations are financed by grants, which are notoriously not ample, I can’t expect the same compensation that I would receive doing medical art. These books give the public information and understanding about nature that I would like to contribute to. Black and white art, being less expensive to publish than color, is preferable for books that have a smaller budget.”

me: “What tools would you recommend for someone who wants to experiment with scratchboard?
Trudy Nicholson: “It’s necessary to use good quality scratchboard such as Claybord made by Ampersand or Essdee, an English scraperboard. All tools should also be high quality. When using ink I prefer Gillott 290, 291 or Hunt 103 pen nibs and Higgins Black Magic ink, or Koh-I-Noor rapidograph pens with their own ink. These tools can be substituted by other good quality makes. As a scratching tool I use x-acto blades #16 and holder. This blade can be held at different angles to make extremely fine white lines or wider lines. It takes practice to master textures. When starting to use scratchboard, patience is helpful.”

me: “Since you work mostly on a white surface, how do you make a flawless transition between light and dark tones?
Trudy Nicholson: “Since scratchboard is a correctable medium, it’s possible to experiment with compositions and textures, which adds to the excitement of doing the artwork and also to the final results. Adjacent textures can be blended eliminating a visible border between them. Even the joining of solid black and stark white can be softened with graduating grays created by crosshatching and stippling. Crosshatching has become for me the staple for creating many textures. Crosshatching is made by crossing a series of parallel lines with another set of parallel lines at an angle. The degree of that angle will determine the resulting texture. A very acute angle will produce a moiré pattern that can give the effect of fur, feathers, distant foliage or water. Other textures can be built on the foundation of crosshatching using either white or black lines or dots over the crosshatched texture.”

Posted in interviews, pen and ink/line, scratchboard, techniques | Tagged: , , , , | 1 Comment »

More on The Bone Room…

Posted by Janet on February 10, 2008

Check this out…

I just came across this video on The Bone Room’s website. It wasn’t there since the last time I visited so I was pleasantly surprised. Here you can get a much better description of the place, and learn how to prepare a sad dead rat skeleton into a nice useful skeleton. Please keep these videos coming!

Posted in miscellaneous, reference, stores/products, techniques, videos | Tagged: , , , , | 1 Comment »

Mouthwash as Pen Cleaner?

Posted by Janet on January 30, 2008

Pen and ink is one of my favorite media. I love the clean lines you can get with a good technical pen, but cleaning Rapidographs is always such a pain. Typically I just use some rubbing alcohol, but when I have pen emergencies and no rubbing alcohol, I go for the mouthwash. It works, and leaves your pen nibs minty fresh. I started buying different kinds of mouthwash just to see which brand works the best. The usual blue/green ones like Scope and Listerine are ok, but I find that Tom’s of Maine mouthwash (which by the way is alcohol free) was able to remove some old ink residues that even rubbing alcohol can’t remove. It’s also clear so you can see your pens better. Now don’t get your hopes up too much because I have yet to find something that completely removes old ink and leaves those pen nibs and plastic ink cartridges shining flawlessly. I’m curious to see if anyone has tried anything else that works.

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