Research Platform Services Blog
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A new 3D Slicer workshop will be run across two half days on the 12th and 13th of April! You can sign up to attend this FREE workshop via the following Eventbrite link.
The use of 3D Slicer is gaining traction around here. Check out a recent guest blog post by Jasamine Coles-Black, about her use of 3D Slicer and their new 3D printing facilities at Austin Health.
And check out my recap of the 3D Slicer workshop stream at ResBaz 2016, where we had a guest appearance by 3D Slicer Chief Architect Steve Pieper and Associate Professor of Radiology Dr. Raúl San José.
Come along to learn about how you can generate 3D models of the anatomy from CT and MRI scan data, and more.
3D Slicer at the Research Bazaar conference, 2016
By Paul Mignone
Me and Cadventure!
The creation, manipulation and enrichment of 3D data are still fledging spaces in the data science field. However with only a small team, the Cadventure stream at ResBaz has made great strides in building research communities around 3D data tools. Looking back over the past 12 months, I’m truly in awe of what my team achieved in such a short time. Let’s look back on the Cadventure team’s achievements:
So many achievements…so little time…
Bear in mind ladies and gentlemen, these achievements were all done before the 2016 Research Bazaar conference. By the time the Cadventurers reached ResBaz 2016 they were full steam ahead:
Looking back, I’m amazed by the number of wins my team has achieved over the last 12 months. I personally couldn’t be more proud! With Louise Van Der Werff taking the helm in April 2016, I have full confidence that the Cadventure team will continue to build the 3D data community, and bring it to the forefront of data science!
We are part of something bigger…
Hi, my name is Nikki and I have joined Research Platforms as an R Research Community Coordinator. My journey into learning programming did not follow a well-trodden path. In fact, if you’d asked me about R a few years ago, I would have asked you if you meant the letter in the alphabet between Q and S. So gather round and let me tell you my story.
https://commons.wikimedia.org/wiki/File:USMC-090910-M-4913M-026.jpg
In Year 12, I had no idea what I wanted to do with my life. I spent many a weekend trolling university open days, looking for inspiration. Inspiration struck at the Melbourne Uni open day, where I did a tour of the Australian College of Optometry and was shown a camera that could take a picture of the back of a person’s eye. That seemed pretty cool to me, so I enrolled in a Bachelor of Optometry at Melbourne Uni.
https://en.wikipedia.org/wiki/Fundus_photography
As I progressed through the degree I began to realise that perhaps clinical optometry wasn’t the right profession for me. I really enjoyed the optics lectures, but with the profession mainly focussed on primary healthcare, optics doesn’t get much air time.
During the final year of my degree I did a research project looking at divided attention. Participants sat in front of a screen with constantly moving stimuli, performing various tasks, while I measured their eye movements. I really enjoyed building a headrest for the chair we were using (which turned out to be extremely uncomfortable for my participants – my bad!) and designing stimuli for the experiment. With my creative side engaged, I decided to enrol in a research degree.
Wanting to venture a little from optometry, but not too far, I did an MPhil looking at the relationship between visual perception and pointing behaviour. The experimental code was written in Matlab by an academic in Adelaide. Having had no prior programming experience, I spent many days trying to work out what each line of code meant, so that I could make small edits of my own.
After finishing the MPhil, I travelled around Europe and the
USA for 6 months, trying to decide what to do next. The resounding response I
received from fellow travellers was that I sounded like I wanted to go back to
study.
Having developed an intrigue into the (what seemed to me then) mystical world of programming, I enrolled in a PhD focused on developing new algorithms for visual field machines. Visual field machines are used to measure vision in glaucoma, mapping out visual sensitivity across space.
With no real programming experience, I spent the first 6 months of my PhD learning basic programming concepts using the language C. During this time, I spent many hours with Alistair Moffat’s text book: Programming, Problem Solving and Abstraction with C.
Once I got my head around C, I needed a way to analyse and visualise my data. Enter R. I would love to say that my ardour for R was immediate, but in reality I had some reservations. Coming from a low-level programming language, it wasn’t immediately apparent to me why R would be useful. I have seriously revised my opinion since then.
Here are some of the reasons why:
Graphic created in R
My route to learning programming has been unconventional, which has given me a unique perspective on programming concepts. I would love to share my R knowledge with you. Watch this space for details of future training sessions.
If you would like to discuss your R problems with me, you can contact me at nikkiR@student.unimelb.edu.au or on twitter @nikkiRubinstein. I look forward to hearing from you!
Guest post by: Jasamine Coles-Black
Hello everyone! I’m Jas, a final year medical student at Austin Health, and one of Dr Louise van der Werff’s 3D Slicer padawans. I can’t believe it’s been 8 months since I was first introduced to the software, via The Research Bazaar’s 3D Slicer Alpha Workshop.
As my background is purely clinical, the first few months were a steep learning curve indeed! Since then, ResBaz has helped me gain the necessary skills to segment DICOM datasets, perform basic modifications in CAD, and 3D print the resultant models. It’s a course that I highly recommend, and I have my eye on other fabulous ResBaz CAD courses, such as Autodesk Inventor, TinkerCAD and Fusion360.
Me as a 3D Slicer virgin, at the 3D Slicer Alpha Course last July.
One of the first tasks I undertook with my newfound segmentation skills was to develop a workflow to create 3D printed aortas from patient CT scans. This involved taking advantage of contrast enhanced CT angiograms. The highly dense contrast circulating the body lights up the vessels of interest like a Christmas tree, as you can see below. This allows me to apply the FastMarch algorithm to quickly and easily isolate the anatomy of interest. With help from Louise, hollow aortic models have also been created
Right: A 3D printed hollow aorta, fresh from our 3D Printing Lab. Left: Segmentation of an aorta using the FastMarch algorithm.
These models will be used to educate trainee surgeons at The University of Melbourne’s Graduate Diploma in Surgical Anatomy about the intricacies of abdominal aortic anatomy, which is difficult to visualise on cadaveric material. This will be undertaken by Professor Chris Briggs, Dr Tarinee Kucchal and Matthew Pappas. 3D printed models of abdominal aortic aneurysms, or triple A’s as we like to call them (abbreviations are half of medicine!), will also be used by Tony Kao to educate patients at the Austin about their disease.
Abdominal aortic aneurysm model generated in 3D Slicer, with and without the surrounding mural thrombus.
Other projects currently under works at Austin Health include the segmentation and printing of patient-specific liver and kidney models to aid surgical planning, the printing of lumbar and thoracic vertebrae as well as flexible trachea models to aid with anaesthetic training. Below is an example of a hollow, 3D printed trachea developed from a patient’s CT scan at Austin Health’s 3D Printing Lab.
A hollow trachea prototype, created in our 3D Printing Lab.
Our efforts have been part of the #3DMed initiative, founded by Dr Paul Mignone of Research Platforms, and Mr Jason Chuen, a vascular surgeon, in 2015. Since then, our two Makerbot Replicator 2X’s have been getting a workout at Austin Health; one resides in our 3D Printing Lab, the other is at the Austin Library and is available for staff use 24/7.
After a few weeks of testing, the @Austin_Health Medical #3dprinting Lab is officially open! Bring us your projects! pic.twitter.com/ZcqmMplxmj
— Jason C (@ozvascdoc)
March 1, 2016
If there is a clinical problem you think 3D printing will be able to help you with, don’t hesitate to contact us at Austin Health. I can be reached at: jahuang@student.unimelb.edu.au.
Last but not least, watch this space for an announcement of this year’s inaugural #3DMed Seminar!
By Aliza Wajih
Oh, what a fantastic experience ResBaz always is, full of fun & surprises!
Last year it was one of my goals to attract as many female participants to attend Inventor CAD class as I could. Through the year I managed to find a few communities like WISE (Women in Science and Engineering) Unimelb and RoboGals and was able to reach it with a 75% majority female class at ResBaz. I was also able to find two brilliant female helpers!
When your CAD class is 75% female! #ResBaz #womenintech @ResPlat @ResBaz @WISEunimelb pic.twitter.com/SfvUbYhoB0
— Aliza w (@awajih08)
1 February 2016
At Resbaz, we had a wonderful group of people from diverse academic backgrounds. We had two artists, Emilie and Tiziana, who plan on using 3D modelling and printing technologies for sculpting. We also had engineers, architects and PhD students. One of our participant, Lisa Giusti, plans on using Inventor to design safety vests for jockeys as an intrinsic case study in the role of design in radical product innovation! Inventor is just the kind of tool she would need!
Proud of my fan realised @ResBaz @unimelb 2016 during Autodesk inventor class!! pic.twitter.com/dw6vaG5Msn
— Lisa Giusti Gestri (@GestriLisa)
2 February 2016
We were a class of about twenty-four people with five helpers. Having this participant-to-helper ratio allowed us to maintain a collaborative space where we could get everyone talking. There were many questions, no hesitations, and a lot of collaboration and mingling. From my point of view, that is exactly what makes a successful workshop!
You can always count on help being available at the Inventor stream! #resbaz @awajih08 @PJMignone pic.twitter.com/s2MSBx2gG3
— Vincent Khau (@thevinniek)
2 February 2016
The Inventor course covered everything from basic sketching skills to complicated sketch designs and assemblies. This time however, we also focused quite heavily on free form modeling - as this feature in Inventor gives designers more ergonomic design capabilities.
Bobby teaching free-form in Inventor at #resbaz pic.twitter.com/OmWeAbdWro
— Vincent Khau (@thevinniek)
1 February 2016
Featured below is our most innovative member, Eve, participating in our Makerspace meditative colouring event!
Beautiful meditative colouring at #makerspace #resbaz pic.twitter.com/4o2DjLHb4F
— Aliza w (@awajih08)
2 February 2016
All in all, ResBaz was another successful event but I could not have done this without my fantastic helpers! Pictured below are Bobby and Vincent , the Inventor training experts from last year, and five brand new additions to our Inventor family: Alison, Melissa, Bentley, Basit and Aston! We had been running intensive training workshops in preparation for ResBaz led by Bobby and I. From the excellent feedback we have received it is evident that everyone’s hard work has paid off.
My awesome Inventor team! Bobby, Bentley, Vince, Aston, Alison & Melissa @ResBaz @alisonmantega @thevinniek pic.twitter.com/z9e2UVSLZE
— Aliza w (@awajih08)
15 March 2016
Lastly, I would like to thank all the participants and helpers for the wonderful experience. I hope Inventor is going to be helpful for you and that you enjoyed this as much as I did!
My #ResFamily! The people behind #ResBazMelb ❤ #ResBaz pic.twitter.com/BpZl6PCQp1
— Dejan (@heyDejan)
5 February 2016
The Inventor course can be found here.
More workshops will be run for Inventor throughout the year so keep an eyen on the calendar if you have missed out on ResBaz!
By Xue Qian and Paul Mignone
Hi everyone! My name is Xue, and I’m a development coordinator for the Melbourne Accelerator Program (MAP). MAP is an entrepreneurship program at the University of Melbourne. In the four years since it was established, MAP has received international recognition for the quality and impact of its program. In November 2015, it was ranked the 8th best university accelerator in the world by UBI index, 2nd in the Asia-Pacific region, and Number 1 in Australia.
I’m passionate about future technology and entrepreneurship. As a development coordinator, I work closely with the entire MAP team to manage, promote and execute many entrepreneurship events. Prior to MAP, I worked in e-commerce, and ran a Student Entrepreneurs organisation. I’ve also recently completed a Bachelor of Commerce at the University of Melbourne.
Last month, I was invited to attend the 2016 Research Bazaar conference to discuss with researchers the potential of commercialisation and start-ups as a career path. Given their large community base, expertise in data science tools and fantastic research translation workshops (i.e., #SharksDen), I believe that the Research Bazaar is perfectly placed to unveil some of Australia’s best talent and ideas for commercialisation.
Me (second from the left) listening to some amazing researchers!
I wasn’t disappointed. After talking to many researchers at the event, not only did I hear some fantastic ideas, I quickly realised that few researchers were aware of their commercialisation potential. Fewer researchers were aware of platforms that could help them commercialise their research. I endeavour to change this, and I would like to use this opportunity to introduce our premier entrepreneurship program that can transform researcher ideas into reality.
So I call to you all researchers and aspiring entrepreneurs!
The MAP program beings again for 2016! Our information night will reveal the nuts and bolts of the application process and other opportunities for aspiring researchers and entrepreneurs.
Tickets are available here: http://bit.ly/1QRLRAF
Our first Start-up Velocity class is also coming up, if you have an idea but don’t know where to start, this program is for you!
Register here: http://bit.ly/21XKiYM
MAP’s vision is to launch great ventures which positively transform the world. The MAP Start-up Accelerator awards 8 start-ups with $20,000 funding, office space, mentoring, and opportunities to pitch in Melbourne, Sydney and Silicon Valley. 24 companies have graduated from the MAP Start-up Accelerator and between them have raised $10 million in funding, created over 200 jobs and generated over $10 million in revenue.
We hope to see you there!
When I started my PhD, almost two years ago, I didn’t know what a Jupyter notebook was, I had never heard of Docker, the Nectar research cloud, or github. After a frenetic ride on this digital rollercoaster, I was able to help deliver a training course last week that assembled all of these crucial components of open, reproducible computational research - a concept we call the web notebook server.
When students sat down for the VIEPS Introduction to Python Course, they used DIT4C as a web-interface to launch Docker containers on the Nectar Cloud.
The docker images we were using included a beefed-up Scientific Python so we could introduce Python’s great mapping capability.
So far so good, we had a class of 26 all with the identical software suite, all running on reliable Nectar infrastructure. As usual the docker containers were by default running Jupyter notebook servers, as our preferred environment for teaching Python.
But what was really novel is that the default address for the Jupyter webserver was not pointing at the notebook port, but at a static website we built into the Docker image. Thus website contains all of the course content, navigation, access to Jupyter notebooks, the shell, etc. Here’s the Docker magic:
jupyter notebook --port=$port --ip=0.0.0.0 --no-browser --NotebookApp.default_url="/files/www/index.html"
At this point it might be useful to take a peek at what the website looked like to a novice Pythonista:
The static website gets built by MkDocs. Like many static site generators it is able to make simple web content from even simpler source content - in this case it renders markdown as HTML.
So did it work? Well, on the whole yes. We pushed our resources a little too hard, running expensive mapping functions. But the result was great output, like this map of global plate motion vectors and strain rate made with Cartopy (see here for a description):
Why would you do this? Well, what we demonstrated is that we can run a workshop style course, all from a single webpage, served from a Nectar VM, and with seamless links to the Jupyter notebook, shell and filebrowser environments. And you can do this without being a web aficionado.
At the heart of this approach is the simple convenience that Course notes sit alongside the Python machinery for putting the ideas into practice. Moreover, you can provide participants with a complex scientific software stack built and archived through Docker
Everything you need to build the VIEPS Introduction to Python course can be found here. Please get in touch if you would like to develop a similar project, or use DIT4C to provision a project like this. We can also provide access to a limited number of containers for anyone interested in checking out the course.
The web notebook server concept was created by Louis Moresi with help from Dan Sandiford. Tim Dettrick provided invaluable assistance in integrating the project with DIT4C.
Python has been transitioning from Python 2 to Python 3 for a ridiculously long time. This question was being asked in 2011 when I was wondering which version I should learn and what the difference actually was.
Currently Python 3 is probably your best bet, as most packages now support it and there are many improvements to the Python language in version 3.
That being said there are libraries that will only work in Python 2 and there is a huge amount of legacy code that has’t been transitioned yet. This might be especially true if you use specialist libraries in your work.
Another reason to use Python 2 is if you are doing the excellent Coursera course by Dr. Chuck which is being converted to Python 3 (I know this because I’m part of the open source project to do the conversion) but is still in Python 2.
For most people the difference between Python 2 and Python 3 comes down to how you print and what happens when you divide something. Printing now requires brackets around what you want to print - just like any other python function.
name = 'Alistair'
print(name)
>>> Alistair
name = 'Alistair'
print name
>>> Alistair
The other one, division, is integer division (where the remainder is discarded) in Python 2 and normal division in Python 3 (use ’//’ to do integer division in Python 3) if the numbers being used are integers. If at least one of the numbers is a floating point number (e.g. 1.5), the division is normal in both.
answer = 10/3
print(answer)
>>>3.3333333333333335
answer = 10/3
print(answer)
>>>3
So for anyone starting out with Python, the difference between the two versions is trivial and I’d suggest using Python 3 by default and Python 2 when you have to.
Python 2 and Python 3 will live happily side by side on a computer but the Anaconda package manager will make this situation a whole lot easier and has many other benefits as well.
So I would suggest installing the Python 3 Anaconda and then setting up a Python 2 environment for when you need it.
Download the version for your OS here and follow the instructions. There is both a command line installer and a graphical installer, so choose whatever you’re most comfortable with.
To setup a second environment like a Python 2 environment, come down to #Hackyhour at Bar Tsubu @Unimelb Parkville campus and we’ll get you sorted out! The instructions are on the Anaconda site too.
I had a fantastic time at ResBaz 2016. It was an exhausting whirlwind adventure and I’m so glad I got to be a part of it.
I ran the 3D Slicer workshop, one of the 8 major streams that ResBaz attendees were allocated to during the event. This workshop was run across the first two days, with a whopping 9 hours of overall content. Phew!
21 people participated in my workshop in total, from a range of different academic backgrounds. Fields of study included archaeology, veterinary science, evolutionary biology, physiotherapy, dentistry, cancer research, medical image processing, food science, biomedical animation, health science communication, and more.
As in previous workshops, the content was mainly focussed around generating 3D models of anatomy from DICOM datasets like MRI and CT scans using medical image processing techniques. We also had a look at 3D volume rendering and visualisation, image registration, statistical analysis, 3D printing, and more.
All attendees bright-eyed and bushy tailed on the first day.
I had two fantastic helpers during the training sessions: Jasamine Coles-Black, a Masters student in the Department of Medicine at Austin Hospital, and Rachel Swain, and Undergraduate student in Biomedical Engineering at Swinburne University of Technology. The girls did a fantastic job at helping out participants during the workshop, and Jas presented a portion of the content to the class, helping the whole workshop run a lot more smoothly.
Me and my awesome helpers Jasamine Coles-Black and Rachel Swain. Thanks guys!
One of the highlights of this workshop for me was the guest appearance by two prominent members of the 3D Slicer worldwide community, a ResBaz first!
Dr. Steve Pieper, is a Computer Scientist with extensive expertise in Medical Imaging, Surgical Planning, and Biomechanical Simulation, and is the Chief Architect of 3D Slicer. Dr. Raúl San José is an Associate Professor of Radiology in Harvard Medical School, and Principal Investigator of the Chest Imaging Platform http://chestimagingplatform.org/, which includes SlicerCIP.
Steve and Raul called in from Boston in the US, and spoke about 3D Slicer and its capabilities, including the Chest Imaging Platform, and presented a number of very interesting use-cases.
The close to 90 minute session was recorded; you can watch it in it’s entirety on the Research Bazaar YouTube channel. In addition, the slides presented by Steve and Raúl can be viewed via the following links.
3D Slicer in 2016 by Steve Pieper. Chest Imaging Platform by Raúl San José Estépar. Chen-GyroGuide-Slicer.pptx by Steve Pieper.
The 3D Slicer online community is extensive and very active, and Steve and Raúl were thrilled to be able to participate in our Melbourne based event from the other side of the world. I have been in contact with Steve Pieper since mid-2015, when I was initially putting together our 3D Slicer workshop material, and he very kindly offered feedback and advice regarding my content. It has been great to come across members of this community who are so willing to share their knowledge and collaborate.
Conferencing this morning with Steve Pieper, Chief Architect of 3D Slicer! @ResBaz #ResBaz pic.twitter.com/PBIJeI4VGE
— Jessica Beach (@JessABeach)
1 February 2016
In addition to this great presentation, I also handed out a prize to one of the workshop participants. For one of our workshop challenges, I had participants generate a 3D model of a child’s trachea from an MRI scan. This is quite a challenging task, with lots of manual segmentation steps required. Will James generated the best looking model, and was awarded the ‘Best Virtual Surgeon’ award, a special ResBaz mug handed out at the awards ceremony on the third day. Congratulations again Will!
Me awarding the ‘Best Virtual Surgeon’ award to 3D Slicer workshop attendee Will James, for his 3D model of a trachea.
Enjoyed learning Slicer, met great people at #ResBaz #ResBazmelb, thanks for Best Virtual Surgeon award! & @PJMignone for 3D printing lab
— Will James (@BioMationViz)
3 February 2016
Overall the experience was a great one. Thanks to everyone who attended, I had a great time meeting you all, and hearing about your research challenges was fantastic.
To see the ResBaz workshop content in full, follow this link.
We will be running more 3D Slicer workshops throughout 2016, so if you missed out during ResBaz, don’t despair. Contact me directly at louisevanderwerff@gmail.com or express your interest for the workshop on our website.