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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
http://goo.gl/HnpAQq
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
http://arxiv.org/pdf/1206.1148v2

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 (http://goo.gl/LTWUf)
Medical Imaging 101 pt 2: CT (http://goo.gl/IHaFw)
Medical Imaging 101 pt 3: MRI (http://goo.gl/UVbiU)
Functional vs. anatomic image (http://goo.gl/UTPK7)
Visible Human project (http://goo.gl/cv2xU)
Eye of Horus post (http://goo.gl/qpxyh)

Image sources other than the above article:
Lung and brain CT images (http://goo.gl/HHhqSJ)

CT Heart (http://goo.gl/eqbFde)
#ScienceSunday  
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You are a troll, Hayden. Goodbye. 
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Police and Thieves by Junior Murvin
Police and thieves in the streets
Oh yeah!
Fighting the nation with their guns and ammunition
Police and thieves in the street
Oh yeah!
Fighting the nation with their guns and ammunition

From Genesis to Revelation
The next generation will be hear me
From Genesis to Revelation
The next generation will be hear me

And all the crowd comes in day by day
No one stop it in anyway
And all the peacemaker turn war officer
Hear what I say

Police, police, police and thieves oh yeah
Police, police, police and thieves oh yeah
From Genesis oh yeah
Police, police, police and thieves oh yeah

Scaring, fighting the nation
Shooting, shooting their guns and ammunition

Police, police, police and thieves oh yeah
Police, police, police and thieves oh yeah
Here come, here come, here come
The station is bombed
Get out get out get out you people
If you don't wanna get blown up

#MusicMonday
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YES
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#GooglePlusNatureChallenge Day 3 of 5
+Gnotic Pasta invited me to take the  #GooglePlusNatureChallenge . You are supposed to post pictures of nature for 5 days.

Here are some harbor seals, Phoca vitulina, from a recent trip to Goat Rock beach, near Jenner, CA. The Russian River meets the ocean at this location which might be why harbor seals like to give birth and wean their pups here. Apparently they return each year. Don't worry, I kept my distance and used the zoom on my camera.

Also, we didn't stay too long. The wind was wicked, easily 30 mph, cold, and any time the sand got kicked up, you were going to get stung by the sand.

I invite +Gray Embry to the  #GooglePlusNatureChallenge unless he's too busy celebrating his birthday.
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:)

I think I could VISIT the Shedd...
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#GooglePlusNatureChallenge Day 2 of 5
+Gnotic Pasta asked me to join the #GooglePlusNatureChallenge a while ago. I kind of dropped the ball due to stuff.

Today's addition is #ForDucksSake  so +Rugger Ducky should join the challenge, time permitting. I took this picture this afternoon and mamma duck was making sure the ducklings didn't get too close to the humans. Some of the other ducklings stayed hidden in the plants.
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We were between two lakes in Minnesota (isn't everyone?) and had mallards in the back garden: http://goo.gl/2PM5Gz
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Like a Viking!
Because I'm getting a lot of mileage out of this in a private share, I release this to the masses like a Viking.

BTW, I updated my biosketch for a grant proposal, like a Viking. (+Rajini Rao knows what I'm talking about.)
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Fluffy was chillin above the fireplace in the next room when it happened...like a viking.
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Spammer
Rex Graham shared two posts with me, i.e., sending notifications. I pasted my standard response to people who do that:

Please see the section
Posting to Public and Notifying only certain people or circles:
http://goo.gl/UW5wV

where it talks about not notifying people who you don't interact with. I don't know you and you don't me. Thank you but I'm not interested in your post. I assume you notified me because you are new to G+. Most people will consider this spammy and either mute you or block you.

My comments were deleted. So I'm going to go out on a limb and say that he's a spammer for his website/company Top Birding Tours. Rex, you're getting bad SEO/advertising advice.
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It's been too long to remember!
🙈🙉🙊
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Blah, blah, blah... ghost town.
Some of my followers are bots. I get that. The rest of you are on G+ for a reason. If you are tired of the ghost town BS, then vote.

h/t +Kee Hinckley 

ETA AdBlocker will likely keep your vote from registering. Thanks +Gert Sønderby 
 
Love Google+? Take a poll to show what a thriving ghost metropolis we are.

via +Agent Questermark​
Google+ is, at the time of writing, still a thing, but its future is far from assured. Unless there's a huge wave of interest, Google+ may not be long for this world. Or perhaps I'm just being pessimistic, and actually people are still interested in Google's social network. There's only one way to find out……
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Hah yes it is, Chad!!!!!
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Hurry up, Exploding Kittens
I want my deck of Exploding Kittens now! Did you order yours? Do you want to come over and play? I hope they make an online version so I can play with my HO friends.
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I'm just old and puzzled now! 
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Taimyr wolf and the origins of dog
There's an ongoing debate about where and when dogs originated. The when part might be closer to an answer now. Genetic drift is used by evolutionary biologist to try to recreate the lineage of species. The discovery of a 35,000-year-old wolf rib bone in the Taimyr peninsula in northern Siberia was the key to this story. The DNA from that bone suggests that it diverged from a common ancestor of present-day wolves and dogs near the beginning of the domestic dog lineage. Their technique uses genetic drift of 'regular' DNA and mitochondrial DNA.

► Genetic Drift
There are non-lethal random mutations in DNA that survive to the next generation due to natural selection and sometimes due to 'luck'. Surviving by natural selection makes sense, a mutation affords an advantage so that offspring should excel and survive. Genetic drift is when a mutation doesn't necessarily result in an advantage but is nevertheless passed on 'by chance'. Tracing these mutations help create a lineage for evolutionary biologists.

► Mitochondrial DNA vs. Nuclear DNA
Mitochondria are the energy power plants inside cells. They have a few genes necessary for oxidative phosphorylation, which is a fancy term for making energy. The nucleus of the cell is where the chromosomes are. Nuclear DNA is the DNA that you hear about in the news, for example in forensic science. In the figure below, you can see that mitochondrial DNA is passed on only by the mother while nuclear DNA is passed along by both parents. Genetic drift in mitochondrial DNA is much slower and helps refine the lineage of a species. It is slower because it is only inherited by half of the genetic source, i.e., the mother.

You can read a summary of the article in layman's terms here:
Arctic find confirms ancient origin of dogs
http://news.sciencemag.org/biology/2015/05/arctic-find-confirms-ancient-origin-dogs

Full article and source of the very cool graphical abstract:
Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds
Skoglund et al
Current Biology May 2015
http://www.cell.com/current-biology/abstract/S0960-9822(15)00432-7

Source for the mitochondria DNA figures:
University of California Museum of Paleontology's Understanding Evolution (http://evolution.berkeley.eduhttp://goo.gl/WZgKRV

A bit more reading:
How the wolf became the dog (full article behind paywall)
http://news.sciencemag.org/environment/2015/04/how-wolf-became-dog

Late for #FidoFriday  but always on time for #ScienceEveryday  
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very intreresting...good
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Flowers at Wat Buddhanusorn in Fremont, CA
We've had a cold spell for about a week so  not many new flowers at my house, since my last #FloralFriday  post. So here are some flowers from CA.
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These are spectacular captures for a phone camera. Nice job on the composition. 
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Chad's Collections
People
Have him in circles
69,763 people
sajid aftab's profile photo
‫عبدالسلام المصري‬‎'s profile photo
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Catherine Wade's profile photo
Kelli Miller's profile photo
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Education
  • Illinois Institute of Technology
    BS Chemical Engineering, 1994
  • University of Illinois at Chicago
    PhD Bioengineering, 2001
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Tagline
I'm the medical imaging, Red Wings, Formula One, Tech guy.
Introduction
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.
Work
Occupation
Scientist
Skills
Medical Imaging methods
Employment
  • 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
Gender
Male
Relationship
Married