Archives For March 2013

When looking at pictures of animals in the wild, one may ask the question: Why are most of these animals brown or black, and why do we see very few colorful creatures? This question can be approached from multiple angles. I will ignore selective pressures that provide an advantage to certain colors. Instead, I will focus on the mechanism behind these colors.

Let’s begin with mammals. When we talk about most creatures being brown or black, we are usually considering mammals, since colors are vibrant across other classes (e.g. reptilia, amphibia, aves). Colors in skin and fur arise from two pigments. They generate two colors: brown-black (through melanin) and reddish-yellow.  I challenge you to use this color palette to make the color green. There are evolutionary advantages to being brown. Early mammals were presumably small, rat-like creatures living on land. It was best to blend into the environment and to invest energy into escape mechanisms. Amphibians, on the other hand, were not limited to the brown dirt of land and were able to develop a green color. This does not answer why they could do this, so let me delve into that.

This is where it gets interesting.

It turns out that birds, amphibians, and reptiles are unable to generate pigments for green (and many cannot generate blue). Most of the tetrapod (four-legged) world is like this.  How, then, could they possibly look so vibrant? The colors arise not from the colors of pigment, but from a molecular refraction mechanism. All of these colors arise from two pigments: black and yellow-red. Thus, when a chameleon changes color, it is not depositing pigments. Instead, it is changing the shape of its refractory cells in order to alter the refraction effect.


In bird feathers, the mechanism is a bit more complicated, but it is the same idea. If you have time, try this experiment: Take some flour, and mix it with water. Mix until the flour is suspended evenly in the water. Now, move the glass to a well-light area. What color do you see? You will notice that the suspension looks bluish-white as opposed to just white. This is due to light scattering. Shorter-wavelength blue light is more easily scattered than longer-wavelength red light. What you then witness is this scattered blue light, giving the suspension a blue tint. Another example is found in compact discs. If you stare at the bottom, you will see not just a silver-coated disc, but an array of colors reflected off the CD’s surface. This is due to the same effect, but we are now looking at scattering from tracks on the CD. Spacing of ridges and orientation of pigment granules in bird feathers generates the same effect. Though the pigments are still black and yellow-red, this scattering provides vibrant colors. If you want to learn more about this, I recommend reading this article on peacock feather coloration.

The aforementioned scattering is known at the Tyndall effect. Simply put, when a suspension of particles is exposed to light, some of this light is scattered and produces interesting colors. The flour/water example I provided was just one. You will also see a blue tint of smoke from the exhaust from some automobiles, also due to a suspension similar to our flour and water. Simply put, longer wavelengths (e.g. reds) are transmitted, but shorter wavelengths (e.g. blues) are reflected. I should note that this is a different mechanism from light scattering seen in the sky at sunset. Whereas scattering in our atmosphere is usually by very small particles (Rayleigh scattering), scattering in colloidal suspensions is by relatively larger particles (Mie scattering). This is important to note because the effects of scattering from larger particles are more vibrant and less subtle.

Mammals are not completely brown and black. An exception to the boring colors of mammals arises in the irises of our eyes. The iris is still composed of melanin, as before. However, the density of melanin determines how opaque or translucent the upper layer of the iris becomes. When more translucent, light can pass through this upper layer and be backscattered by layers below. As before, shorter wavelengths of light are more likely to be scattered. This, in turn, results in blue irises.

Like the example above, many questions in this world are nuanced, and these nuances make the questions (and answers) more interesting.

For the first part of this series and to learn a bit more about 3D reconstruction of computed tomography (CT) slices, check out NEURODOME I: Introduction and CT Reconstruction. Our Kickstarter is now LIVE!

“As I stand out here in the wonders of the unknown at Hadley, I sort of realize there’s a fundamental truth to our nature. Man must explore. And this is exploration at its greatest.” – Cdr. David Scott, Apollo 15


It is official. Our Kickstarter for NEURODOME has launched. I have already described a bit about my role in the project and described CT reconstruction. Future posts will delve into fMRI imaging and reconstruction, along with additional imaging modalities and perhaps a taste of medical imaging in space. You might be surprised at the number of challenges astronauts had to take while aboard rockets, shuttles, and the ISS. All of this will be part of the NEURODOME series.

With our launch, we hope to raise enough funds to develop a planetarium show that illustrates our desire to explore. To do so, real data will be used in the fly-throughs. Our first video, The Journey Inward, provides a basic preview of what you might expect.

I will continue to post about this project but, for now, read about NEURODOME on our website and, if you can, help fuel our mission!

A Troubling Divorce

March 23, 2013 — Leave a comment

The unhappy marriage between the United States government and science (research, education, outreach) ended this month. We’ve known for years now that the relationship was doomed to fail, with shouting matches in Washington and fingers pointed in all directions. I would more likely describe an end to the relationship between elected officials and human reason, but that would be harsh, and I still have hope for that one. Sadly, this generation of congresspeople signed the paperwork for a divorce with science.

America’s love affair with science dates back to its origins. Later, Samuel Slater’s factory system fueled the Industrial Revolution. Thomas Edison combatted with Nikola Tesla in the War of the Currents. It was a happy marriage, yielding many offspring. The Hygienic Laboratory of 1887 grew into the National Institutes of Health approximately 50 years later. We, the people, invented, explored, and looked to the stars. Combined with a heavy dose of Sputnik-envy, Eisenhower formed the National Aeronautics and Space Administration (NASA) in July 1958. We, the people, then used our inventions to explore the stars.

Since then, generations of both adults and children have benefited from the biomedical studies at the NIH, the basic science and education at the NSF, and the inspiration and outreach from NASA. Since Goddard’s first flight through Curiosity’s landing on Mars, citizens of the United States have not only directly benefited from spin-offsbut also through NASA’s dedication to increasing STEM (science, technology, engineering, mathematics) field participation. Informed readers will know that although the STEM crisis may be exaggerated, these fields create jobs, assuming benefits from manufacturing and related careers. Such job multipliers should be seen as beacons of hope in troubling times.

Focusing on the NIH, it should be obvious to readers that biomedical science begets health benefits. From Crawford Long’s (unpublished and thus uncredited) first use of ether in the 18th century through great projects like the Human Genome Project, Americans have succeeded in this realm. However, as many know, holding a career in academia is challenging. Two issues compound the problem. First, principal investigators must “publish or perish.” Similar to a consulting firm where you must be promoted or be fired (“up or out”), researchers must continue to publish their results on a regular basis, preferably in high-impact journals, or risk lack of tenure. The second problem lies in funding. Scientists must apply for grants and, in the case of biomedical researchers, these typically come from the NIH. With funding cuts occurring throughout the previous years, research grants (R01) have been reduced both in compensation per award and number awarded. Additionally, training grants (F’s) and early career awards (K’s) have been reduced. Money begets money, and reduction in these training and early career grants make it even more difficult to compete with veterans when applying for research grants. Thus, entry into the career pathway becomes ever the more difficult, approaching an era where academia may be an “alternative career” for PhD graduates.

The United States loved science. The government bragged about it. We shared our results with the world. Earthriseone of my favorite images from NASA, showed a world without borders. The astronauts of Apollo 8 returned to a new world after their mission in 1968. This image, the one of the Earth without borders, influenced how we think about this planet. The environmental movement began. As Robert Poole put it, “it is possible to see that Earthrise marked the tipping point, the moment when the sense of the space age flipped from what it meant for space to what it means for Earth.” It is no coincidence that the Environmental Protection Agency was established two years later. A movement that began with human curiosity raged onward.

Recently, however, the marriage between our government and its science and education programs began to sour. Funding was cut across the board through multiple bills. Under our current administration, NASA’s budget was reduced to less than 0.5% of the federal budget, before the cuts I am about to describe. The NIH has been challenged too, providing fewer and fewer grants to researchers, forcing many away from the bench and into new careers. Funding for science education and outreach subsequently fell, too. Luckily, other foundations, such as the Howard Hughes Medical Institute, picked up part of the bill.

I ran into this problem when applying for a grant through the National Institutes of Health and discussing the process with my colleagues. I should note as a disclaimer that I was lucky enough to have received an award, but that luck is independent of the reality we as scientists must face. The process is simple. Each NIH grant application is scored, and a committee determines which grants are funded based upon that score and funds available. With less money coming in, fewer grants are awarded. Thus, with cuts over the past decade, grant success rates plummeted from ~30% to 18% in 2011. When Congress decided to cut its ties with reality in March and allow for the sequester, it was estimated that this number will drop even further. (It should be noted that a drop in success rate could also be due to an increase in the number of applications, and a large part of that decrease in success rate over 10 years was due to the 8% rise in applications received.) This lack of funding creates barriers. Our government preaches that STEM fields are the future of this country, yet everything they have done in recent history has countered this notion. As an applicant for a training grant, I found myself in a position where very few grants may be awarded, and some colleagues went unfunded due to recent funding cuts. This was troubling for all of us, and I am appalled at the contradiction between rhetoric in Washington and their annual budget.

Back to NASA. As we know, President Obama was never a fan of the organization when writing his budget, yet he spoke highly of the agency when NASA succeeded. Cuts proposed by both the White House and Congress to NASA in 2011 for a reduction of $1.2 trillion over 10 years have already been in place. This was enough to shut down many programs, reduced the number employed, and led to the ruin of many of its buildings. However, the sequester, an across-the-board cut, also hit NASA very hard. As of yesterday, all science education and outreach programs were suspended. This was the moment that Congress divorced Science.

All agencies are hit hard by these issues, and it isn’t just fields in science, education, and outreach. Yet, speaking firsthand, I can say that these cuts are directly affecting those of us on the front line, trying to enter the field and attempting to pursue STEM-related careers. Barriers are rising as the result of a dilapidated system. Having had numerous encounters with failed F, K, and R awards amongst friends and colleagues simply due to budget constraints (meaning that their score would have been awarded in a previous year, but the payline was lowered to fund fewer applications) and seeing children around New York who are captivated by science education but are within a system without the funds to fuel them, I can comfortably claim that we are all the forgotten children of a failed marriage.

Whether it be due to issues raised in this post or your own related to the sequester, remember that this is a bipartisan issue. There are no winners in this game, except for those congresspeople whose paychecks went unaffected after the sequester. I urge you to contact your elected official. Perhaps, we can rekindle this relationship.

Those who work closely with me know that I am part of a project entitled Neurodome ( The concept is simple. To better understand our motivations to explore the unknown (e.g. space), we must look within. To accomplish this, we are creating a planetarium show using real data: maps of the known universe, clinical imaging (fMRI, CT), and fluorescent imaging of brain slices, to name a few. From our web site:

Humans are inherently curious. We have journeyed into space and have traveled to the bottom of our deepest oceans. Yet no one has ever explained why man or woman “must explore.” What is it that sparks our curiosity? Are we hard-wired for exploration? Somewhere in the brain’s compact architecture, we make the decision to go forth and explore.

The NEURODOME project is a planetarium show that tries to answer these questions. Combining planetarium production technology with high-resolution brain imaging techniques, we will create dome-format animations that examine what it is about the brain that drives us to journey into the unknown. Seamlessly interspersed with space scenes, the NEURODOME planetarium show will zoom through the brain in the context of cutting edge of astronomical research. This project will present our most current portraits of neurons, networks, and regions of the brain responsible for exploratory behavior.

To embark upon this journey, we are launching a Kickstarter campaign next week, which you will be able to find here. Two trailers and a pitch video showcase our techniques and our vision. For now, you can see our “theatrical” trailer, which combines some real data with CGI, below. Note that the other trailer I plan to embed in a later post will include nothing but real data.

I am both a software developer and curator of clinical data in this project. This involves acquisition of high-resolution fMRI and CT data, followed by rendering of these slices into three-dimension objects that can be used for our dome-format presentation. How do we do this? I will begin by explaining how I reconstructed a human head from sagittal sections of CT data. In a later post, I will describe how we can take fMRI data of the brain and reconstruct three-dimensional models by a process known as segmentation.

How do we take a stack of images like this:


(click to open)

and convert it into three-dimensional objects like these:

These renders allow us to transition, in a large-scale animation, from imagery outside the brain to fMRI segmentation data and finally to high-resolution brain imaging. The objects are beneficial in that they can be imported into most animation suites. To render stacks of images, I created a simple script in MATLAB. A stack of 131 saggital sections, each with 512×512 resolution, was first imported. After importing the data, the script then defines a rectangular grid in 3D space. The pixel data from each of these CT slices is interpolated and mapped to the 3D mesh. For example, we can take the 512×512 two-dimensional slice and interpolate it so that the new resolution is 2048×2048. Note that this does not create new data, but instead creates a smoother gradient between adjacent points. If there is interest, I can expand upon the process of three-dimensional interpolation in a later post.

I then take this high-resolution structure mapped to the previously-defined three-dimensional grid and create an isosurface. The function takes volume data in three dimensions and a certain isovalue. An isovalue in this case corresponds to a particular intensity of our CT data. The script searches for all of these isovalues in three dimensions and connects the dots. In doing so, a surface in which all of the points have the same intensity is mapped. These vertices and faces are sent to a “structure” in our workspace. The script finally converts this structure to a three-dimensional “object” file (.obj). Such object files can then be used in any animation suites, such as Maya or Blender. Using Blender, I was able to create the animations shown above. Different isovalues correspond to different parts of the image. For example, a value/index of ~1000 corresponds to skin in the CT data, and a value/index of ~2400 corresponds to the bone intensity. Thus, we can take a stack of two-dimensional images and create beautiful structures for exploration in our planetarium show.

In summary the process is as follows:

  1. A stack of saggital CT images is imported into MATLAB.
  2. The script interpolates these images to increase the image (but not data) resolution.
  3. A volume is created from the stack of high-resolution images.
  4. The volume is “sliced” into a surface corresponding to just one intensity level.
  5. This surface is exported to animations suites for your viewing pleasure.

This series will continue in later posts. I plan to describe more details of the project, and I will delve into particulars of each post if there is interest. You can find more information on this project at