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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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+Susana M.​, just send me a message if you have any questions. 
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Happy #FidoFriday.
Ana was enjoying the long grass just before I cut it. 
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Exercise is good. 
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Anniversary post, like a Viking
I'm imaging radioactive cells, like a Viking. How about you?
This post is about a year old and needed to be revisited.
 
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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Fed my fish LIKE A VIKING.
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Counter-punch? We're talking about misogyny not a fart
I dearly miss Jon Stewart but Trevor Noah isn't as bad as I expected. Whether it's Stewart, Noah, Oliver, or Wilmore, why are the news satirists doing better than the real journalists?
The Best F#@king News Team recreates highlights from Donald Trump's interview with Megyn Kelly.
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+Chad Haney She wasn't combative, and i think that people expected that. Maybe she should have been. I find it hard to get things done that way. Besides, what would it have accomplished? He's not changing, good or bad, and we know his record. She is aiming to be Fox's Barbara Walters, so she addressed him in a way that might further her goals. She owes the public nothing. Think about this: If she was a guy, we would probably call her a wuss for making a big deal out of it. However, since she's a woman, she's expected to be butt hurt and carry a feminist flag for all of us. That's not what I need. I can do that or not do that myself. Feminism is about choices and opportunities. She choose to do it her way. She asked the pig/women question briefly. Good enough. She moved on in a way that may encourage others to be interviewed, thus, promoting her career. That's a choice. She owes us nothing and that's not Patty Cake. She must have known she would receive blow back.
Journalist are not really the heroes and avengers that the movies make out. They have private ambitions.
This interview changed nothing of our perception of him but might have smoothed her career path. Besides, what did we want from that interview? A brawl? Now that would not be journalism. She got him on camera. He exposes himself. Job done.

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Numbers - Kraftwerk
Another classic from the 80s.
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Sweet Home, Chicago
It's good to be home. I just got back from the Midwest Preclinical Imaging Consortium in Madison, WI. My brain is full. Madison is a nice town with a great campus. Time for me to catch up at work. 
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I will let her know, thank you!
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I'm going to have to try some of these these.
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+Carissa Braun Oh, it was. And for me it was double fun. I was in the Army (a noncomm) at the time, and all the other guys in our group were Naval officers.

The Scouts adult leaders training program is simply awesome.
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Trolls:0 Amy Schumer:1
After a photo of Amy Schumer at the beach in a bathing suit brought out the worst in the internet, she fires back with an Instagram post.
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+Paul Lamoureux​, she's awesome. 
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FOIA tool for harassment
I've posted before about +Kevin Folta's previous FOIA episode.
https://plus.google.com/u/0/+ChadHaney/posts/96vXnYoykFM
I guess when science isn't on your side, you use tactics like senseless FOIA requests until the scientists give up.
 
At what point does the FOIA stop being used for legitimate uses and starts being a tool for one egomaniacs paranoid obsession with herself. Good luck +Kevin Folta
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+James Salsman, sort of. The Food Babe gave a talk at Kevin's university and he challenged her story that she answered questions afterwards.
http://kfolta.blogspot.com/2014/12/vani-hari-food-babe-and-silencing.html
There are other instances where the Food Babe and her army have gone after Kevin.
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Prize Money - Birocratic
A little bit more chill. 
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Hey DJ - World Famous Supreme Team
Welcome to the 80s.
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+Michelle C​, what's up next? 
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No surprise +Terry McNeil figured it out. It's imported salted French butter. It tastes really good on fresh bread.
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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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  • landshark-zenkoi
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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.
Collections Chad is following
Education
  • Illinois Institute of Technology
    BS Chemical Engineering, 1994
  • University of Illinois at Chicago
    PhD Bioengineering, 2001
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