Category: MiVIP

Parent category for MiVIP posts

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MiVIP meets AI…

Well, I think it was inevitable. My data science lab has slowly crossed over to the dark side into the world of  Machine Learning and Artificial Intelligence.


Let me apologize for being MIA for so long. Life has been pretty hectic these past months as I have been building the MiDATA program here in the Department of Medical Imaging at the University of Toronto. The good news is that the MiVIP program will now be inviting students to participate in machine learning and artificial intelligence in medical image research.


This summer will include the launch our our MiStats+ML program where we will have students from the department of statistical sciences, computer sciences, and life sciences all work together on ML/AI projects in the MiDATA lab.


Stay tuned as we ramp up and get back to some our previous threads like MiWORD of the day…




See you in the blogosphere,




Pascal

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“Hour of Code… Part Deux” at the University of Toronto

What hour of code? What code?

The Hour of Code is a global movement reaching tens of millions of students in 180+ countries. The purpose is to to demystify “code”, to show that anybody can learn the basics, and to broaden participation in the field of computer science. Please see here for more info.

I belong to Code.org a non-profit dedicated to expanding access to computer science, and increasing participation by women and underrepresented students of color.

On Thursday, December 7th, 2017 at 9:30AM we will be hosting our second 
 
“MiDATA Hour of Code at UofT“

What is the purpose of this event?

To engage young minds and help them see the exciting possibilities computer programming can offer them in their future careers.

Who is coming?

Over 100 students (grades 7 to 11) from Central Toronto Academy (TDSB), St Francis Assisi and St Ignatius of Loyola (TCDSB).

Who will be engaging them (so far)?

University of Toronto:
MiDATA (Data Science unit from the Department of Medical Imaging)
*Prof Pascal Tyrrell – Director, Data Science

*Prof Anne Martel – Medical Biophysics (Machine Learning)

*Daniel Eftekhari – MSc student (medical image machine learning)

*Dr Mariam Afshin – Research Physicist

*Rasha Mahmood – VBIRG

Department of Medical Imaging
*Dr Alan Moody – Radiologist and Chair of the Department

Department of Statistical Sciences
*Prof Paul Corey – Senior Biostatistician
*Chris Meaney – Biostatistician

Department of Computer Science
*Prof Steve Engels

 

Industry:
IBM Watson Health and Merge Healthcare

   *George Gorthy – Senior Sales Consultant IBM Watson Health Imaging
    *Marwan Sati – VP of Development, Clinical Speciality Solutions, Merge Healthcare
*Aditya  Sriram – Developer, IBM Watson Health Imaging

Microsoft (Big Data and Analytics)
* Sage Franch – Microsoft Canada

SAS Canada
*Mark Morreale – Lead, Academic Program

Community:
Ladies Learning Code – Yaa Otchere

 

Industry Support:
Google

Tyrrell lab students and Computer Science undergraduates will be acting as ambassadors.

Where and when will the event be held…exactly?

University College Media Room (RM 140 and RM148) from 9:30 AM to 1 PM

University College, University of Toronto
15 King’s College Circle
Toronto, Ontario

 

Interested in participating? Contact me at pascal.tyrrell@utoronto.ca!

See you all there,

Pascal Tyrrell

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MiDATA hosts “Hour of Code” at the University of Toronto

What hour of code? What code?

The Hour of Code is a global movement reaching tens of millions of students in 180+ countries. The purpose is to to demystify “code”, to show that anybody can learn the basics, and to broaden participation in the field of computer science. Please see here for more info.

I belong to Code.org a non-profit dedicated to expanding access to computer science, and increasing participation by women and underrepresented students of color.

On Wednesday, December 7th at 10AM we will be hosting the inaugural

“MiDATA Hour of Code at UofT”

What is the purpose of this event?

To engage young minds and help them see the exciting possibilities computer programming can offer them in their future careers.

Who is coming?

Over 100 students (grades 7 to 11) from Central Toronto Academy (TDSB), St Francis Assisi and St Ignatius of Loyola (TCDSB).

Who will be engaging them (so far)?

University of Toronto:
MiDATA (Data Science unit from the Department of Medical Imaging)
*Prof Pascal Tyrrell – Director, Data Science

*Prof Anne Martel – Medical Biophysics (Machine Learning)

*John Harvey – Information Architect

MiNE (Medical image Network Enterprise, Sunnybrook Health Science Centre)
*Dr Mariam Afshin – Research Physicist
*Rasha Mahmood – VBIRG

Department of Medical Imaging
*Dr Alan Moody – Radiologist and Chair of the Department

Department of Statistical Sciences
*Prof Jamie Stafford – Statistician and Chair of the Department
*Prof Paul Corey – Senior Biostatistician

Translational Research Program /Institute of Medical Science
*Prof Joseph Ferenbok – Program Director

Department of Computer Science
*Prof Francois Pitt

Faculty of Engineering
*Prof Naomi Matsuura – Department of Materials Science & Engineering

Industry:
IBM Watson Health and Merge Healthcare
*Steve Schudlo – Executive Director, Strategic Alliances, IBM Watson Health Imaging
*Marwan Sati – VP of Development, Clinical Speciality Solutions, Merge Healthcare
*Aditya Sriram – Developer, Watson Health Imaging, IBM

Microsoft (Big Data and Analytics)
*Mark Godfrey – Cloud Architect, TSP – Cloud & Data Center, Microsoft Canada

AceAge
*Spencer Waugh – CEO AceAge
*Sam Campbell – CTO AceAge
*Dylan Horvath – Cortex Design President

SAS Canada
*Mark Morreale – Lead, Academic Program

Community:
Ladies Learning Code – Yaa Otchere

Tyrrell lab students and Computer Science undergraduates will be acting as ambassadors.

Where and when will the event be held…exactly?

University College Media Room (RM 140 and RM148) from 10 AM to 1 PM

University College, University of Toronto
15 King’s College Circle
Toronto, Ontario

 

Interested in participating? Contact me at pascal.tyrrell@utoronto.ca!

See you all there,

Pascal Tyrrell

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The story behind Connectory…

So, you are reading our blog thinking Pascal is a nut – that much is clear – but what of all the students plugged into his group? Are they nuts too?


Well maybe, but today I am going to talk to you about the group of four (not the group of seven) who started small and grew to be Connectory. John, Maria, Natasha, and Roger met in a graduate course at the University of Toronto and decided to work together on a project about innovation. That’s when they met me, joined “the program”, and got busy! Starting any endeavour from scratch is no easy task. All four had never met before, all came from very different academic backgrounds, and though their initial project was for “credit” the rest was on their own time.


There were some rough times at first but with perseverance comes success and Connectory was born and is just finishing up its first project as a new start-up business. Wow! 


Essentially Connectory is a data management solutions software development consulting group that operates in the healthcare space. Check out their webpage here.


Ok, so what? Well this post is not only to congratulate these four on a job well done but also to encourage you to do the same. One thing is for sure: if you don’t try you will not succeed – ever. My programs are all about learning, trying new stuff, benefiting from your successes as well as your failures, and wait for it… giving back. Yup as Uncle Ben said in Spiderman: “With great power comes great responsibility“. 


Just wanted to share a good story from our group with you today.




Listen to Bulletproof by La Roux to get pumped and…


… I’ll see you in the blogosphere!




Pascal Tyrrell

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The Importance of Research

There’s more to the field of medical imaging than a bunch of stuffy radiologists huddled around a couple of monitors. As I mentioned before in my previous post about the history of the imaging technique, the field has undergone a rapid technological advancement in the past century or so, improving the clinical model of visualization. But let’s take a step back from all the scientific stuff for a brief second and look at these developments in a
slightly different light.

During the early stages of medical imaging, X-rays were able to provide people with an initial view of the internal structure of the human body. As limited as that first view may have been, it still played a pivotal role in both challenging and changing people’s perceptions on the human body – to the point where these details would eventually become common knowledge. Without all the major advancements in medical imaging, we could well expect to still be living in the dark.
To really hammer this point home, further advancements in the field would only continue to build on our understanding. What was once the accepted view of the human body has now been given a complete overhaul, thanks to the availability of imaging devices able to produce higher-resolution cross-sectional pictures.

The SparkNotes illustrated version of this post
So what’s the common thread in all of this? Research, of course. While the idea of research leading to new and exciting developments is a pretty basic concept in and of itself, it’s still an important one to keep in mind. Although the field of medicine is comprised of many different sectors, even at the base level there are plenty of opportunities to contribute meaningful ideas and suggestions. Just because you’re an undergraduate student, that doesn’t stop you from devising an independent thesis in an area you’re passionate about. Granted, I don’t want to be too idealistic here, given the logistics of funding, but an interesting and relevant pitch to your primary investigator
could go a long way. Who knows, you may find yourself presenting your findings at a research symposium, complete with nifty results and statistics to showcase your efforts.

The bottom line is, a little can go a long way, and if you already have a keen interest in science to start contributing as soon as possible. The entire medical field is driven by people with a knack for research and discovery – and while there’s never a shortage of great minds, there’s always room for more.
Thanks for reading,
Brandon Teteruck
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The Key to Research: (Key)Words

Do you ever hear a good song on the radio, catch some of the lyrics, and try to type in those lyrics into Google or Youtube to find that particular song you rocked out to on the way home? When that happens and you Google it, do you ever count  how many options you need to pass until you hit the right song? 


Yes, you are not the only one, many people use Google to further explore some of the things they have come across throughout daily encounters. For each instance google is used, whether it be for a song or for neuroscience research and analysis, one thing remains in common: keywords. 


Keywords are essential when searching for various types of information, and the options appearing on any search engine are dependent on the keywords given. How does one establish appropriate keywords for a search engine entry? 
For instance, if one wants to find out more about medical imaging, perhaps using those exact words would give one a head start in finding information. If one wants to find out about the modalities of medical imaging, typing in ‘modalities of medical imaging’ may also be helpful as well. The tricky part becomes when searching for specific uses and studies of the use of those modalities, in medical papers. In any medical search engine, like PubMed, keywords can make or break a search, and are very specific, as the many sections of medical imaging involve many specific factors and details that differ from each study. So next time you decide to search something, whether it be as general as ‘medical imaging’ or specific as ‘cost effective analysis of CT scans,’ just remember that those keywords may give you what you need, or lead you to a place you don’t want. 
Keep (re)Searching!




Faith Balshin 
Follow us on Twitter! @MiVIP_UofT  
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A Crash Course in Medical Imaging

Oddly enough, there’s been a surprising lack of content about medical imaging on a blog with medical imaging in its title. So in order to fill that void, I’ll be providing a brief history on the development of the clinical technique used to visualize the human body.

The advent of medical imaging dates all the way back to 1895, following the discovery of X-rays by the German physicist, Wilhelm Conrad Roentgen. The first X-ray picture was then produced, detailing the skeletal composition of his wife’s left hand. However, the actual quality of this imaging process was still very primitive, only allowing for the visualization of bones or foreign objects.

    Much to Dr. Roentgen’s pleasure, Mrs. Roentgen
    had not discarded her wedding ring
    It was not until the 1920’s that radiologists would develop a more effective method of visualization. This process, known as fluoroscopy, involved either an oral or vascular injection of a radio-opaque contrast agent, which would travel through the patient’s gastrointestinal track. Radiologists could then take films tracking the agent, allowing them to view blood vessels and digestive tracks alike.

      By the 1950’s, imaging procedures progressed towards nuclear medicine, involving radioactive compounds. These compounds were administered to patients because they could be absorbed by cellular clusters being invaded by tumours. As compounds decayed and emitted gamma rays, the recorded radiation could then be detected by gamma cameras, signalling the location of any cancerous developments. 
          The 1970’s were a period of rapid advancement for the field, as a number of modern imaging techniques were developed for clinical practice such as: 

            • Ultrasound – Uses sound waves that are able to penetrate cellular tissue. Once they reflect off the body’s internal organs, the vibrations generate an electrical pulse which can then be reconstructed into an image. 
            • PET-CT Scan – Positron emission tomography (PET) uses compounds that emit positrons when they decay rather than gamma rays. It is now combined with a computed tomography (CT) device to generate a high-resolution image displaying sectioned layers of the scanned area. 
            • MRI – A Magnetic Resonance Imaging scanner runs a strong magnetic field through the body, aligning hydrogen protons. As the protons return to their original position in the atom, they generate radio waves, which are then picked up by the scanner and used to create an image based on signal strength. 

            Fast-forward to present day and over 70 million CT scans, 30 million MRI scans and 2 billion X-rays have been performed worldwide! The field of medical imaging is still growing by the day, with ongoing research leading to new developments.

              Thanks for reading,

                Brandon Teteruck 
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                Researcher’s Dream: Katy Perry Edition

                What happens when you put a famous pop superstar with various Billboard number one hit singles as an endorser for a medical field involving teeth, mouth and gum surgeries? 
                A Katy Perry-odontist!
                And no, I am not insinuating the likelihood of Ms. Perry giving up her “Hard Candy” tour and making her way down to Harvard Med for a doctor of dental surgery specializing in periodontistry, but in reality, when researching, there are a lot of weird combinations of research that actually lead to a plausible conclusion!
                Take cost effectiveness of MRIs, CT scans and ultrasounds. There are many variables pertaining to which machine is more cost effective, but in order to find that out, the research being done with regards to the cost involves stepping OUTSIDE THE BOX and figuring out unique key factors that all contribute to the cost, timing, and effectiveness. One must observe not only the actual cost of the machine, but also the condition the patient is in and the situation of the effected area. In order to look at that, maybe some family history must be dug up. And there you go! A whole research perspective on family history of certain patients, just to figure out cost effectiveness of a certain machine. Weird combination of research if you think about it, but in the end, very effective in reaching somewhat of a conclusion to the research question, just like the medical imaging equipment should be doing in the first place! Do not underestimate the lengths in research it takes to solve the question at hand, and always think outside the box, because you never know what you will find, and someday, maybe Katy Perry will open up her own clinic, and sooth patients with her very own soundtrack!
                Keep Researching and Singing, 
                Faith Balshin 
                Don’t forget to check out MiVIP’s twitter account, @MiVIP_UofT! 
                Comment on what you think are weird research combinations if you dare! 
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                REsearch and Destroy!

                Why do we need to find out things, shouldn’t we be content with what we have already, why does research matter? Well, simply put, we conduct research because we are eager human beings looking to seek further knowledge into any task or question presented to us. Human beings in general are inquisitive beings that become fulfilled when they accomplish something and the information spectrum is broadened. To accomplish almost any goal, whether it be recreational or academic, information through research is required. Research essentially helps humans, be human. We question, research and come up with an answer, and that in itself is a true accomplishment.

                Research, like any other entity, has its ups and downs. You can follow the processes, look in the right books, but come up with the wrong information. When that happens, do not give up your search, rather organize it another way. Even if that seems to be time wasted, it was not, because the amazing thing about seeking knowledge is even if it’s the wrong knowledge found, one still learns from ANY obtained information. Research is a definite experience, and something valuable is ALWAYS learned when conducting research, whether it be the information being searched for, or a bit of self growth. And the best part? There is no time limit to knowledge. So get started. Just remember your keywords.

                Faith Balshin
                Check out MiVIP’s official twitter account! @MiVIP_UofT
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                Research Read-ables: Library Edition

                How in the world does someone actually get to researching something, it seems too complicated! Well, fear not my friends, research comes in all letter shapes and information sizes! For a beginner researcher, an easy and effective start would be to go to a library. The library holds a haven of information, from fictional stories for experience to non fictional magazines, dictionaries and novels. The library is a great place to start looking for answers, the librarians are able to guide anyone to the right factual source of data that will provide good information, and no, they aren’t from the dinosaur era (even though you may think you’re in that era while searching through books).. 

                Many educational researchers use books and even textbooks to help with research projects, papers and various journals. I know I can always trust my school librarian, she always gave me the best books and information, even if she didn’t remember my name.

                 Even though libraries are ‘so 90s,’ it wouldn’t kill you to walk into one, you definitely will learn something.  

                Keep Reading!
                Faith Balshin 
                Follow us on twitter for the latest updates of the program! @MiVIP_UofT