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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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Happy #NationalDogDay.
Ana playing with the super lure, ie, her favorite fetch toy. 
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I do now. Our lime green hydrangea bloomed big time this year. The one like yours, not at all. Who knows why...
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I got mine, get yours
Do you like my GOP title? Seriously, if you missed the Kickstarter campaign, go buy a set.
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+Carissa Braun, I think one is enough. As +Jess Nut, said, it's fast enough that you can rotate people in.
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Camping at Interlochen State Park 2015
I was waiting for G+ to make a nice Story from my camping trip. Unfortunately it made two separate stories, one of them titled Cedar Springs, MI, which was where I stopped at a Meijer grocery store for lunch items. I couldn't add the proper photos to either of the two Stories, so here you go. The old fashioned way.

My two person tent from REI was big enough for my wife and me and Ana. I got to try my new sleeping bag from REI. It's super lightweight for backpacking. The temperature at night didn't get below 50 °F so I was too hot in my new bag, until about 3 AM each night. Ana had her own 'travel' bed. My cousin had some old carpet that we used for the entrance of the tent and also for Ana to lay on. Park rules required her to be on leash all the time. So we often had her on her super long leash, tied to a tree. She really enjoyed looking for chipmunks. I saw some raptors up in a dead pine tree next to my tent on the first day, while setting up camp. I couldn't get a good picture but they looked like peregrine falcons.

We ate pretty well. I got to try out my new Primus backpacking stove. It worked really well and boiled water super fast. I just bought a larger pot for it this morning (0.5L to 1L).
Foil packets for dinner:
Cod, onion, butter, lemon, dill, parsley, paprika
Hobo stew: ground beef, Veg-all, cream of mushroom, seasoning
I'll probably bring couscous next time. We also picked up some fresh corn at the local grocery store and cooked that on the fire too. One night my cousin made Italian sausage with caramelized onions and bell peppers. I brought plenty of craft beer.

Traverse City is nearby so we took a day trip there. Unfortunately not cherry season, so we couldn't go cherry picking. The first pub we tried for lunch didn't want to set up an outside table for Ana. We tried a few other places and ended up across the street at Union Tap and Grill.
ControversiAle from Shorts Brewery was so delicious I had a second, to make sure it was reproducible.
https://www.shortsbrewing.com/beers/controversiale/
The fried pickle appetizer was a hit.  Sweet pickle, cheese, wrapped in ham, then deep fried in beer batter. My Ruben sandwich was OK. Their homemade chips (not fries for my British friends) were pretty good. My wife thought that the lobster roll sandwich was too rich so we passed it down the table after I helped finish some of it.

Mission Pointe Lighthouse and Hessler Log cabin was the next stop. A storm had gone through a few days earlier so there were tons of trees and power lines down. Sleeping Bear Dunes was hit hard. We would have been staying there if it weren't booked when we tried making reservations, several months in advance.

The next day we went canoeing along the Platte River to Sleeping Bear Dune. We tipped over when I was trying to keep us 'docked' at a rest stop. Ana made it very unstable as she moved around, sometimes rapidly. My sister's boyfriend also fell in when they ran into a log. He tried to push away from it.

On the last day we just went hiking around the campgrounds. We decided not to swim any of the time there because of Swimmer's Itch. There's a parasite that enters the lakes via bird poo. When the parasite enters a snail, only there can it reproduce. Since it reproduces in snails, you are more likely to get it in shallow water. The parasite can't infect humans but you can get a nasty rash from it. There are some species that can infect dogs so we decided no swimming for us or Ana. You can read more here.

http://www.mayoclinic.org/diseases-conditions/swimmers-itch/basics/definition/con-20030150

http://www.cdc.gov/parasites/swimmersitch/biology.html

Heterobilharzia americana
http://www.capcvet.org/capc-recommendations/canine-schistosomiasis-heterobilharzia-americana

Sadly my Exploding Kittens arrive the day we were driving to Interlochen, MI.
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Nice story.  Always better to do things yourself than to rely on some computer program to do it for you.
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#LazyPlus: Cell phone holder
I'm 99% sure I'm going to order a Moto X Pure edition when Moto Maker is ready for orders. I'm looking for recommendations for a holder for my car. Let me know if your recommended cell phone holder sticks to the windshield or not. I don't think I want to glue or use any adhesive on the dash, but you can try to convince me if your cell phone holder is the greatest thing since sliced bread.
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+Chad Haney​ I've used both the custom fit holder with charger and the universal holder. The custom fit holders were for my Note 2, OnePlusOne, and Galaxy S4. They all fit like a glove. An exellent product, well worth the money.
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I want a giant Lite-Brite
Anyone who has a sensory childhood memory of making endless light-peg designs with a Lite-Brite will find himself instantly transfixed with Everbright, an interactive LED-lit board inspired by the original toy. “Everbright is a giant toy for people who never want to stop creating,” the folks at San Francisco–based Hero...
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Hell yes!
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Have him in circles
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Chad Haney

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Perspective on the Paleo diet.
“What going Paleo really means”
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Well, it is Thorsday.
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+Addison Rennick​, you are right. I hate them as they stink like crazy. My wife enjoys them in her soup, hence the noodles in the picture. 
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The Foo Fighters Rock!
This is so freaking awesome. 
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14 X
I wish the #WhiteSox  could be more consistent so that Chris Sale's efforts don't keep going to waste. Ten years ago they won the World Series. It's not looking so good at the moment, so I hope it isn't another 10 years before the next championship.
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Lately the Sox have not been worth seeing, well, except when Chris Sale is pitching.
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Endangered Elements
See helium in the top right corner? Helium is important for MRI and MRI is important to literally see what's wrong with people. Think about it before buying a helium filled balloon. I wrote more about the helium reserve here:
https://plus.google.com/u/0/+ChadHaney/posts/99SpR28xBme
 
Today's post is a collaboration with the American Chemical Society's Green Chemistry Institute, looking at some of the 'endangered' elements on the periodic table. Learn more about them here: http://wp.me/p4aPLT-1o4
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There's a very simple solution to this. Make it more expensive. 
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I'll probably get the 2-person tent, since Big Agnes gets good reviews.
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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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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.
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Male
Relationship
Married