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

Archive for the ‘photography/imaging’ Category

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:

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.


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:

…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.

*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 »

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.


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 »

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:

Thanks Sarah for the heads up!

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

Eureka Photography Award

Posted by Janet on August 24, 2008

Winning images from the New Scientist Eureka Prize for Science Photography is now touring Australia, starting with the Australian Museum at Sydney. This year, the top three winners are Phred Petersen, Steven Morton, and Katrina Putker. For details, see the links below.

About the winners and the competition:

About the exhibit at the Australian Museum:

An article featuring this year’s first place winner, Phred Petersen:;ID=1y91ikeo5sic

Last year’s article featuring last year’s first place and this year’s second place winner, Steven Morton:

Photos by other winners (scroll to the bottom):

Posted in photography/imaging | Tagged: , , | Leave a Comment »

DNA Art at MoMA Store

Posted by Janet on May 21, 2008

DNA print

For about $500, you can have your DNA profile printed and framed through the Museum of Modern Art online store website, putting a new spin on the concept of family portrait. This full service is offered through a company called DNA 11, which controls the entire process from running a gel to the printing and varnishing. Artists who work on your print even sign the back to ensure authenticity. A swab kit is provided with each purchase to collect a sample from you, a family member, a pet, or anything that contains DNA (but why would you want to pay $500 to frame chicken liver DNA?). Once the company receives your DNA sample, it can take up to six weeks to deliver your high-quality print.

Speaking of DNA art, the MoMA store also features DNA-inspired jewelries by Andrea Valentini such as this bracelet shown below. Earrings and necklaces are also part of this collection.

DNA bracelet

Posted in photography/imaging, stores/products | Tagged: , , , | Leave a Comment »

Edward S. Ross

Posted by Janet on April 22, 2008

Edward S. Ross, curator emeritus of entomology at the California Academy of Sciences, is the leading entomologist studying insects of the order Embiidina, web-spinning insects related to stoneflies, termites, and earwigs. Now ninety-three years old, Edward Ross continues to publish his lifelong study in comparative anatomy of embiids.

Lifetime Expedition
As a young boy, Edward Ross collected numerous insects–over 50,000 by the time he graduated high school. However, due to the influence of his father, an artist specializing in pen and ink illustration, Ross initially planned to become an illustrator. When he realized that illustrators spend most of their times indoors, he took a quick turn to entomology and eventually earned a Ph.D. at U.C. Berkeley for the study of Embiidina in 1941.

During World War II, while serving as a 1st Lt-Major, Ross worked on mosquito identification and malaria surveys in New Guinea and Philippines. It was during this time that he met and took interest in tribal cultures. This interest continues and over the next few decades he would photograph people of all ethnicities on his travels.

After the war, Ross returned to the California Academy of Sciences where he previous worked for a brief period. For his studies, he traveled to Central and South America, Africa, Asia, and Australia while publishing numerous works. Upon his return from the Andes in the early 1950s, he took up insect photography and wrote the book “Insects Close Up” based on his photographs. The majority of the 50s and 60s were spent outdoors. From 1970 to 1975, Ross taught insect biology at U.C. Berkeley.

Ross now has approximately 350,000 embiids in his collection and works in the home that he began to build following World War II. He continues to build additions to the house (with some help from others) to house his works. Until the past few years, the majority of embiid drawings were made by Ross himself. With the help of many illustrators in recent years, new illustrations of unpublished species are being made and his illustrations are being archived into digital format.

Ross is in the process of writing a book on insect-flower relationship. He also plans to write a book on people of the world. He still publishes journal papers and holds exhibits for his photography works.

The next post will cover my recent visit with Edward Ross, including images of his illustrations and a recent publication. Here is a list of links on Dr. Ross:

Publication list:
Interview by Bay Nature, 2005:
Entomologist David Rentz’s blog entry:
Some insect photography work:
An Article by Ross in California Wild:

Posted in interviews, photography/imaging, zoological | Tagged: , , , , | 4 Comments »