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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)
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+Susana M.​, just send me a message if you have any questions. 
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Deliberate, Y'all been Rick Rolled
I think it's definitely plagiarism and it's deliberate to get free media attention. It's working.
Plagiarism is distracting from the epic Rick-Roll embedded in Melania Trump's speech. (Trump campaign has a mole.) Embedded image. 10:28 PM - 18 Jul 2016. 1555 Retweets1362 Likes. Reply to @DennyBurk. Replies. Jeff Lawrence. 7h7 hours ago. Jeff Lawrence @jeffdlawrence. @DennyBurk ha.
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Well there's sorry and then there's Canadian sorry.
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How ‘Citizens United’ is helping Hillary Clinton win the White House
It's a long but somewhat interesting read.

“Wouldn’t you know that Hillary Clinton has become one of the greatest beneficiaries of the Citizens United Supreme Court decision,” Citizens United President David Bossie said. “It is an irony that is not lost on me.”

Priorities USA Action
Ready for Hillary PAC (now Ready PAC)
Correct the Record
American Bridge 21st Century
These four core pro-Clinton super PACs have together raised more than $86 million toward Election 2016.

“We found a way to raise significant amounts of money from small donors,” said Briggs, adding that Sanders’ average contribution today is still close to, if not exactly, the $27 figure Sanders loves to tout from the campaign trail. “Clinton’s super PACs — it’s clearly a way for her to raise a lot of special interest money from a system that’s corrupt. This reliance, and the secrecy, raises the same questions that are raised about why she won’t release transcripts of her paid speeches to Wall Street executives.”

I'm closing comments because it's late and apparently that's what people do when they post something about HRC.
Reforms wait as Democratic front-runner targets GOP with super PACs, ‘dark money’.
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Finally the water is warm enough
The water temperature was about 70 °F. The last two years around this time, the water temperature was closer to 60 °F, #ThanksObama  (polar vortex). A day late for #FidoFriday  but Ana had fun.

Lake Michigan water level is up about 0.4 m or 1.2 ft compared to 2 years ago. So there isn't any beach (I know it's rocks) where we take Ana to swim. It was a little too windy and choppy for us to swim with her. I was worried about the rip currents so we threw her toy just far enough for a few strokes and then Ana could reach the ground again. We'll try again when the water is more calm or maybe find another location.
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She used to paw at the door bc she wanted to be right there with me. She was a royal PITA tonight, so she got it back good. Wouldn't leave us alone, so she got the cuddly stuffed animal treatment. That lasts only so long for her.
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Add this to 2016 sucks
We need stability in that region. A coup doesn't seem to help with stability in a volatile region. I wonder what +Gnotic Pasta  thinks.
Turkish military says armed forces have "fully taken control" of the country to protect the democratic order and maintain human rights.
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I totally agree, +Brigitte W. 
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FYI, CV Contact Info
If you submit a CV/resume without any contact info on it, chances are the employer/screener isn't going to bother to look it up.

ETA
HR just called me and said that this went through a temp agency and they likely stripped the contact info out, so that we cannot hire the person directly. They are likely protecting their finders fee. Ugh.
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+Chad Haney I did just now ;)


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#LazyPlus question about old programming languages
For my fellow old timers, can you think of a programming language where you cannot directly assign a variable to a new variable and therefore have to use a for loop?

Instead of:
newThingy = oldThingy;

This code someone sent me does this (in MATLAB):
for i=1:256
newThingy(:,:,i) = oldThingy(:,:,i);
end

SMH

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Reminds me of the ministry of silly walks.
https://www.youtube.com/watch?v=iV2ViNJFZC8
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Have him in circles
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Both political parties need reflection
I'm surprised I'm re-sharing an article written by a Republican who was part of the Reagan and both Bushs' administrations. Mr. Wehner makes several interesting points and some of them are equally valid for the blue team. I'm starting to think that I'm actually an Independent.
The struggle for the nomination is over, but the struggle for the soul of the party is not.
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When I resigned, I stated that I am not conservative and neither was the Party of Lincoln, which dismantled the traditional institution of of slavery.
I won't be defined for their fundraising and convenience. (What color shall we be? Glitter!)
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So the people who chose Jill Stein over Hillary are what? They can't be sexist. Maybe they don't like Hillary the person, not Hillary the woman. Just like I don't like Sarah Palin the person, independent of the fact that she is female. By the same logic of this blog post, isn't it possible that Gloria Steinem and Madeleine Albright are just as sexist, blindly supporting Hillary the woman and not Hillary the person?

As I mention on my previous Hillary post, apparently you're supposed to close comments.
 
Food for thought.

The Left’s enthusiastic embrace of these tropes and rhetoric props up the narrative that, for a woman to have reached the upper echelons of power in her field, she could only have done so through depravity and deception. Her success is undeserved, and she is therefore unworthy — and dismissing Clinton’s campaign as a “coronation” only gives credence to a culture that has for so long cheered the brutal teardown of accomplished women.

Hillary Clinton is indeed, as her critics claim, part of the “the establishment.” Like all women of lofty ambition, she is keenly and woefully aware that in 2016, less than a century out from women’s suffrage, pioneering into a space formerly only occupied by men requires an acceptance that gender constrains one to work within the system, rather than from outside of it.

So the next time you say, “I hate Hillary Clinton,” ask yourself why.

(comments closed)
It’s time liberals acknowledge that their vitriol toward the presidential candidate is hurting women — and speaks to something deeper
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Swimming in Lake Michigan with my dog
Google Photos was timely in these two "remember.." collages. I included a photo of my wet day pack from today, thanks to Ana shaking on it. You'll notice that the beach and rocks are totally submerged in today's photos (separate post).
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+Brigitte W., most of the time she is.
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Yea, that checks out, no problem.
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AFK, closing comments just in case.

Chad Haney

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Double or triple ply?

h/t +Ray of Sunshine 
 
omg some of this stuff is fantastic! 
From Sexual Connotations to a Resemblance With White Supremacist Signs
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OMG those were good! And I then followed with the update following the Trump/Pence announcement today - Pence is probably feeling like Christie was after endorsing Trump, the zombie on the stage. I almost feel sorry for Pence, but not really. After all, he said yes. 
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Chad's Collections
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Have him in circles
70,186 people
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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.
Basic Information
Gender
Male
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Married
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  • landshark-zenkoi
Story
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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