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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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+Jose Muniz Jose gue pasa quillo
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Kick Insomnia
I'll have to remember this trick when I travel. I get insomnia when I travel. I found this via Shankar Vedantam on Twitter. I always enjoy his tidbits on +NPR. Check out the video to learn how your arteriovenous anastomoses could help you sleep.
#ScienceEveryday  
Let the Science of Us Sleep Institute offer you a helping foot.
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+Chad Haney​ New Englander here, I sleep with my feet exposed year round (except when I'm trying to sweat out a cold, or flu)
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Do you speak python?
I know Peo does, right +Kimberly Chapman​.
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Well she's always on about the 8 bus here, which is quantum, in that it appears and disappears from schedules.
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Piyush "Bobby" Jindal
I thought this was a very interesting video. It's just another reason, Bobby won't go far. Not understanding checks and balances, i.e., why there are three branches of government is pretty bad.
http://www.msnbc.com/msnbc/bobby-jindal-lets-just-get-rid-the-court
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I feel the same way about Michelle Malkin. Thank dogness she's not running for president.
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Do you even science bro?
I can't tell you how much I f#!&ing love this article from The Allium. I even read the title.

Thanks to +Rajini Rao for pointing me to The Allium.

ETA
I should mention the Do you even science bro? joke is from +Nic Hammond  from this post.
https://plus.google.com/u/0/+ChadHaney/posts/97yKScnyDU5
Toronto, Canada - Undergraduate student and science major, Laurel Ann Hardy admitted today that she didn't even understand the I F*&%$ng Love Science article that she just shared on Facebook. W
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I was probably harsh toward the "uninitiated crowd" in my prior comment.  There are of course degrees of growth in the acquisition of the knowledge and the development of properly poised passion for science.  There is also certain elements of "light" or "popularized science" that if done right, are indeed appealing and even entertaining, again if the facts presented are not a distortion but rather a simplification of complex theories, to make them appealing to the public at large and encourage/excite the young generation and indeed the public at large at wanting to dig up and know more about various scientific disciplines.

However what is troubling is the glorifying of a culture of excessive shallowness and superficiality at the expense of a more poised approach toward scientific news (indeed also many other things in life).  Even worse are those elements that exploit this age of glorified shallowness and superficiality for their own gains, thus promoting those traits and perpetuating facts and factoids that have little or nothing to do with science at best and that are pseudoscience passed for science or myths and fantasy/falsehoods at worse.
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Black Man, White Man (Take Two) - Alton Ellis
Powerful song. #AskRachel  do you really know what Alton Ellis is singing?

#MusicMonday  
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+John Azi, maybe you missed the #AskRachel  hashtag for Rachel Dolezal.
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Have him in circles
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#FloralFriday 3 July 2015
A cool and wet spring has led to more mosquitoes than flowers. No sign of my dahlias or clematis yet.
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Me, too, but that sounds likely.
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Screwed, update from my doc
Here's an update from my doc appointment today. My surgeon suggests another surgery. He wants to remove the plates and screws and break my wrist again. Yes, you read that correctly. One of the bones has healed at the wrong angle. It's causing occasional bone on bone contact and will lead to arthritis soon.

The procedure is kind of cool. They will take an x-ray CT of my right wrist and make a mirror image of it. Materialise, a company in Belgium, will calculate the precise location to cut/break the bone and 3D print a jig that will be used during the surgery. You can see how this amazing technology works here:
https://vimeo.com/105016337 (try the Materialise website if the Vimeo video doesn't work, http://www.materialise.com/check-out-our-videos).
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Oh! Should check that out. Thanks Gary.
 
+Chad Haney the good stuff makes you comfortably numb. Kinda.
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D'aww, the little fledglings are losing their down.
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Take it easy with the fireworks
My dad has PTSD from the Vietnam War so I appreciate this sign.
For Russell Cook, a combat-wounded Army veteran with post-traumatic stress disorder, the barrage on his overloaded senses begins with fireworks explosions in his Valrico neighborhood as the calendar turns to July.
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+Gray Embry, I think it means, try to do less or farther away from a house with that sign. Also preferably at a reasonable time and not all week. It also probably means don't use M80 "cherry bombs".
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Rangpur Marmalade Update
First, the USPS basically kicked the box of rangpur from California to Illinois. That's based on how the box looked. Now look at the route the last package headed for London took. I understand that the International Service Center (ISC) for Chicago might not be in Chicago. The USPS website states that ISCs are nearby Chicago, New York, Miami, etc. I'm sorry but Des Moines, IA is not what I would call nearby Chicago. SMH

If you missed the main post:
https://plus.google.com/u/0/+ChadHaney/posts/cibzPracrDj
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Phimset
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FYI, Mississippi, it's 2015
The Confederacy remains a part of the identity of Southern states
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Good posting!! Generally speaking, when one country defeats another, doesn't the victor pretty much eliminate all identity of the defeated?  How long was the Nazi flag allowed to be flown over Germany after the Germans were defeated? 
Granted, the USA's treatment of the South when the Civil War ended was something less than stellar (to put it mildly).  (Of course we had to contend with Bill Quantrill - so the sword cuts both ways LOL)

However, the USA has never outlawed flying the Confederate Flag.  Robert E Lee had his USA citizenship restored in 1975.  Jefferson Davis - 1978
Yes, these concessions might be considered minor, but when will the South "let up" just a bit?
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Chad's Collections
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Have him in circles
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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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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.
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Male
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Married