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Chad Haney
Works at Northwestern University
Attended Illinois Institute of Technology
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Chad Haney

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Medical visualization, it's what I see and do
I was going to summarize an article about the history of medical visualization that was discussed in MIT Technology Review in 2012.
The Future of Medical Visualisation
However, I think that the #OpenAccess  article that they reference does a good job on its own. It's kind of strange to think of a review of a review of a review article.
From individual to population: Challenges in Medical Visualization

Rather than review the review of the review, I'll add a few comments and answer your questions. So read either the MIT Tech Rev article or the journal article and ask questions. This is an opportunity to talk to a scientist that works in the medical imaging field.

The article mentions multi-modal volume visualization. If you have been following my  #CHMedicalImagingSeries then you know that each imaging technique (modality) has strengths and weaknesses. Combining imaging modalities, like the MRI and CT below of my head, allow you to take advantages of the strengths and minimize the weaknesses. To get the best out of multi-modality imaging you need to be able to fuse the images. The technical term is image registration or some like image co-registration. There is a lot of research in just this technique to make it more automated. One common technique is called mutual information. Our brains can easily tell that the dark material in MRI is bone (e.g. my skull) and it should match the bright material in CT. Mutual information tells the computer to consider that bright could equal dark by normalizing the images first. The principal axes of the objects are also used to register (align/fuse) the two images. For therapy planning, both surgery (cosmetic) and tumor resection/radiation, multi-modality imaging can have a huge benefit. They mention that in 1993 Altobelli used multi-modality imaging to visualize the possible outcome of complicated craniofacial surgery.

Another use of medical imaging visualization is virtual colonoscopy. Visualization tools that you need are surface/volume rendering, skeletonization, and segmentation.
UCSF Radiology: What Virtual Colonoscopy CT Scans Look Like

Surface/volume rendering is just what it sounds like. The data is analyzed and the surface can be identified and displayed with shading and lighting such that it looks 3D. You can make it true 3D with the right equipment (3D glasses, 3D monitor, and software to split the data into left and right views) but that's not essential. It can't be emphasized enough that modern GPUs have made these difficult calculations become trivial. Some of the early animation work and medical image visualization required high end UNIX workstations. Now that same level of visualization can be done with a low-end gaming PC.

Segmentation is also, just as it sounds. There are automated and manual segmentation tools. For example in the heart and skeleton images below, the tissue of interest has been segmented out of the "background" tissue, e.g., the internal organs, muscle, etc. Again, there is research in this technique alone. Our brain can look at a medical image and identify parts of the brain or organs quickly. "Teaching" a computer program to do that automagically is very difficult, especially if there is motion due to breathing. In that case, you may have to use image registration to get rid of the motion blurring first.

Skeletonization is a process of identifying paths. For colonoscopy, that would be teaching the program to traverse the path of the colon. I've done work where we were measuring blood vessel diameters in a pulmonary hypertension model. Skeletonization was used to automatically identify each part of the vascular tree. From there, it was easy for the software to measure each diameter.

The first three images are fused images of a CT and MRI of me. The yellow surface rendered part is from CT as it shows bone (skull) very well. The grey-scale part of the image is MRI which shows soft tissue very well. The rest of the images are from a Toshiba 320 slice CT. In CT technology, a ring of detectors is used capture the signal from the x-ray source. Each ring is called a slice in clinical CT machines. For a while 64 slice was considered the best. Now 256 and 320 slice machines are becoming available. More slices means you can cover a larger area in a shorter amount of time. So highly detailed images of the heart can be acquired without motion artifacts from the beating heart. Likewise for the lungs.

Here's a few older posts that will hopefully help you understand the article.

Medical Imaging 101 pt 1 (
Medical Imaging 101 pt 2: CT (
Medical Imaging 101 pt 3: MRI (
Functional vs. anatomic image (
Visible Human project (
Eye of Horus post (

Image sources other than the above article:
Lung and brain CT images (

CT Heart (
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You are a troll, Hayden. Goodbye. 
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Why Can’t I Touch It - Buzzcocks
I don't know why this song makes me act like I'm 12 years old again.

Well it seems so real I can see it
And it seems so real I can feel it
And it seems so real I can taste it
And it seems so real I can hear it
So why can't I touch it?
So why can't I touch it?
Then it looks so real I can see it
And it feels so real I can feel it
And it tastes so real I can taste it
And it sounds so real I can hear it
So why can't I touch it?
So why can't I touch it?
Then it looks so real I can feel it
And it feels so real I can taste it
And it tastes so real I can hear it
And it sounds so real I can see it
So why can't I touch it?
So why can't I touch it?
Now it is so real I can see it
And it is so real I can feel it
And it is so real I can hear it
And it is so real I can be it
So why can't I touch it?
So why can't I touch it?

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First Snow 2015-2016
It's the wet heavy snow that made shoveling with one hand a real workout. 
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+Chad Haney that sounds awesome! I want to go after Thanksgiving.
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Ironic, ya think?
This is a bloody brilliant update to a classic.

Big time h/t to +Robyn Miller (from that other place).
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Who is my neighbor?
An Evangelical missionary who helps relocate Syrian refugees mentioned the parable of the Good Samaritan on NPR yesterday. How many Christian presidential candidates, governors, and congressman are really following the Bible when it comes to helping the refugees?
I'm closing comments because I don't have time to 'debate'. I just want people to read the short attached article and reflect on if they are really good Christians and still have no compassion for the refugees.

He asked Jesus, “And who is my neighbor?”

In reply Jesus said: “A man was going down from Jerusalem to Jericho, when he was attacked by robbers. They stripped him of his clothes, beat him and went away, leaving him half dead. A priest happened to be going down the same road, and when he saw the man, he passed by on the other side. So too, a Levite, when he came to the place and saw him, passed by on the other side. But a Samaritan, as he traveled, came where the man was; and when he saw him, he took pity on him. He went to him and bandaged his wounds, pouring on oil and wine. Then he put the man on his own donkey, brought him to an inn and took care of him. The next day he took out two denarii and gave them to the innkeeper. ‘Look after him,’ he said, ‘and when I return, I will reimburse you for any extra expense you may have.’

“Which of these three do you think was a neighbor to the man who fell into the hands of robbers?”

The expert in the law replied, “The one who had mercy on him.”

Jesus told him, “Go and do likewise." (Luke 10:29-37)
12 verses about loving immigrants, refugees and displaced people.
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A good sandwich is one of the finer pleasures in life.
That one looks quite good, especially those tomatoes. 
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Have him in circles
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Chad Haney

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Mostly nonviolent protests as far as I know. I'm sure the video will be all over the news. I saw some Tweets that a few of the rally organizers have been detained. I'll know more in the morning.

@kathychaney's Tweet:
G Bousoño @GBouso1. @kathychaney why protest when the cop is being charged. He is guilty 100%. Sorry, Twitter is taking too long to load. Try again. Home · Sign up · Log in · Search · About. Not on Twitter? Sign up, tune into the things you care about, and get updates as they happen.
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BaSO4, X-ray Contrast
Many of you have probably seen the post by +Mindy Weisberger showing the awesome CT images of various animal's vasculature. The main point of that article is the development of a contrast agent for x-ray computed tomography (CT).

Since I haven't had time to post to my Medical Imaging Collection, I figured I'd take the opportunity to clear up a few things about the technology and stop neglecting my medical imaging collection.

There are two main classes of x-ray contrast agents. Iodine based agents and barium sulfate (BaSO4) based agents. Iodinated agents are typically given intravenously (IV) and sometimes orally. BaSO4 agents are only given orally for live patients/animals. Iodonated agents are soluble in water and often look like water (not very viscous). BaSO4 agents look like thick milk of magnesia (very viscous). There are many reasons why BaSo4 cannot be given IV (viscosity, osmolarity, etc.). BaSO4 agents are routinely used in about 5 million x-ray procedures in the USA. Its use can be traced back to 1910. Iodinated agents are used in around 20 million procedures (Chem. Rev 1999, 99, 2353-2377).

The agent in the article is called BriteVu, developed by Scarlet Imaging. It's a BaSO4 based agent with minerals and silica added. I plan on purchasing some to see what makes it superior to plain BaSO4 or even if it is superior. So the first thing to correct in the article is that this isn't noninvasive in the sense that it can't be used in vivo. It's noninvasive but it's terminal. I think most people assume when you say noninvasive that you also imply survival.

The second misleading issues is that clinical scanners can image fast enough for iodine based agents to work. This is only applicable for animal work where there is only one or two scanners that are as fast as clinical CT scanners. So what does speed have to do with iodinated agents? Unlike BaSO4 agents, they diffuse out of the vasculature very rapidly and are cleared from the body rapidly (relatively speaking). A preclinical scanner does not have a slip-ring like a clinical scanner and therefore is much slower. By the time the x-ray source and detector have traveled around the animal, the agent is already diffusing out. The math used to reconstruct the images would break down because you have an important feature (the vasculature) changing over the time course of the image. See the links below for more information about slip-rings. This is unlike motion artifacts (e.g. breathing) that can be corrected for.

In two of the images below of a mouse, Kiessling et al show that an iodinated agent can be use in vivo with a live mouse. Their prototype slip-ring preclinical scanner is probably over $1million. Nevertheless, it is possible to image fast enough to use iodine in vivo in an animal. You will see that they image the mouse with an iodinated agent, iomeprol 400, on the right side and BaSO4 on the left side for comparison. Keep in mind, the left side image is only possible as a terminal experiment. The other mouse figure shows a 3D rendering to demonstrate how you can visualize the vasculature of a tumor on a mouse. The other five images are from Scarlet Imaging.

Mindy's post:

More information about CT and slip-rings.
Medical Imaging 101 pt 2: CT

Fast CT from GE Healthcare

Image sources:
Scarlet Imaging

Volumetric computed tomography (VCT): a new technology for noninvasive, high-resolution monitoring of tumor angiogenesis
Kiessling et al Nature Medicine 10, 1133 - 1138 (2004)
7 September 2004; | doi:10.1038/nm1101

Duke University has an experimental microCT that can be used to image mouse hearts, which beat up to 600 bpm.
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You are welcome +Lucas Appelmann 
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Once again, opt-in by default instead of opt-out.
Don't want your photos used by Google? You better check your settings.
Just an FYI - I was looking at the settings, and saw that now the default setting is to allow Google to use your posted photos on their products. You have to opt out by sliding the switch.

Don't want your photos featured?
By default, your publicly shared photos may be featured as background images on Google products. You can choose to not have your photos be featured by changing this setting using a computer or mobile browser.

Go to the Google+ settings page.
Scroll to the Photos and Videos section.
Check the box or turn on the option next to "Don’t feature my publicly-shared Google+ photos as background images on Google products & services." If this setting is checked, your photos (including previously featured photos) will not be featured as background images.
Note: It may take several minutes for the change to take effect.
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+Chad Haney mine is a slider with one side gray and the other blue.
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From the book" Sapiens, a brief history of Humankind":

"Experts disagree about the exact date, but we have incontrovertible evidence of domesticated dogs from about 15,000 years ago. They may have joined the human pack thousands of years earlier. Dogs were used for hunting and fighting, and as an alarm system against wild beasts and human intruders. With the passing of generations, the two species co-evolved to communicate well with each other. Dogs that were most attentive to the needs and feelings of their human companions got extra care and food, and were more likely to survive. Simultaneously, dogs learned to manipulate people for their own needs. A 15,000-year bond has yielded a much deeper understanding and affection between humans and dogs than between humans and any other animal. 4 In some cases dead dogs were even buried ceremoniously, much like humans."
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I shared a picture of a sandwich yesterday because my wife can't understand how I can eat a sandwich for lunch nearly everyday. I think as long as you have good cheese and good bread, you're OK. I'm not going to pretend that I make gourmet sandwiches like +Terry McNeil but they are kicked up a notch. I often add some spices to my tomatoes as you can see in the photo.
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I don't know, looks good to me. 
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New UI Circle Management
Anyone figure out how to manage circles with the new UI? When you enable Circle Streams, you only get the top six circles. I don't know about you, but I have way more than six. With Chrome on Win8, I can't scroll or see more than the first six circles to choose from. So I figured I'd just move the ones I really need to see into the top six positions and no bueno, no-can-do.
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If Circles go away, then G+ becomes as shitty as FB.
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Have him in circles
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Medical Imaging methods
  • Northwestern University
    Research Professor, 2012 - present
    Managing Director of the Center for Advanced Molecular Imaging
  • University of Chicago
    Research Professor, 2002 - 2012
    In charge of pre-clinical nuclear imaging. Lead multiple cancer research projects involving pre-clinical imaging.
Basic Information
I'm the medical imaging, Red Wings, Formula One, Tech guy.
I'm a scientist/engineer interested in image based biomarkers, i.e., non-invasively visualizing disease or response to therapy. I mainly research cancer using MRI, PET/SPECT/CT, and EPRI but I'm also interested in cardiovascular research.

Sports: Big formula one fan, Detroit Red Wings, Chicago Bears, and Chicago White Sox.

Music: I like pretty much everything except country. Big fan of Pink Floyd. Bob Marley is a god-like-hero. I love house music when I'm programming or doing image analysis. Miles Davis is a mutical genius (say it in Gumby's voice).

Misc: love dogs, science/technology (gadgets), cars, bicycling... Also Member of The Incorrigibles.

My passion is science and science is my career choice, so I am grateful to be a co-curator for #ScienceSunday.

Don't circle me if you are not open minded and interested in science. I'm very much against the anti-intellectualism/anti-science movement.

There is a cult of ignorance in the United States, and there always has been. The strain of anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that "my ignorance is just as good as your knowledge."
     Isaac Asimov, column in Newsweek (21 January 1980)

A few more hashtags for me #CHMedicalImagingSeries
Bragging rights
There's a whole country named after me. I also developed a blood substitute when I was a graduate student.
Collections Chad is following
  • Illinois Institute of Technology
    BS Chemical Engineering, 1994
  • University of Illinois at Chicago
    PhD Bioengineering, 2001
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