Research Platform Services Blog
Month
By Aliza Wajih
The best part about working at ResPlat is that I get to do a lot of exciting things and work with many amazing people. My proudest achievement so far is building a community with Women in Science and Engineering (WISE)! So far we have worked together for ResBaz, TinkerCAD, 3D printing training and a recent fun end-of-semester de-stress event.
I started collaborating with Jess Vovers the president WISE at the end of last year when she helped me promote my ResBaz training and get as many female designers to join Inventor by advertising Resbaz on twitter, facebook and the WISE newletter. If you would like to read more about it click here.
A happy happy bubble blowing president ✨✨✨ pic.twitter.com/fIhwBvy9sp
— WISE (@WISEunimelb)
25 June 2016
Yes, she is just a magical as she looks!
Around that time we also organized a TickerCAD and 3D printing class for early March. TinkerCAD was a new software for me this year, but thanks to Vincent’s classes I was able to learn and teach it. I got to work with some amazing and creative women.
Slight screaming. #3dprinting excitement with @ResPlat ✨ pic.twitter.com/i95QF4nOI2
— WISE (@WISEunimelb)
5 April 2016
Of course, I didn’t do it alone! My team, Vincent and Louise were there as helpers and with their support we did a pretty decent job!
Learning!! @ResPlat #tinkercad #3dprinting training and workshop. So awesome to make things! pic.twitter.com/C7zhIIgKGg
— WISE (@WISEunimelb)
5 April 2016
Last week, we hosted a de-stress event at the colab with WISE. with a special guest! Meet the cutest puppy in the world, Toast!
It was great to see some new and old faces and build new connections. I got to meet everyone from women doing their PhD in astrophysics to civil engineer and first year science students! We had a great time playing with Toast, bubbles, colouring, talking and eating! Guess who got to meet the president of Women in ICT? Me.
So I went to the de-stress event with @WISEunimelb on Saturday! Guess who is still pretty happy on a Tuesday? pic.twitter.com/SD4DQ29P5f
— Aliza w (@awajih08)
28 June 2016
Hopefully we will continue doing great things together with WISE! Here is to a good break and a great next semester! See you all soon :)
Fun with @WISEunimelb chill out! @ResPlat pic.twitter.com/5q5DPwYYlN
— Aliza w (@awajih08)
25 June 2016
Post by: Jasamine Coles-Black
A sneak peek into Austin Vascular, home to
@unimelb’s new #3DMed #3DPrinting facilities @UniMelbMDHS @Austin_Health pic.twitter.com/s9yo03tHYC
Medical 3D printing is really taking off at Austin Health! Following the launch of our Austin 3DMed Lab, we have introduced our 3D Slicer for Beginners courses to the hospital, with our first course on the 18-19th July selling out overnight. Following the additional courses that we have set up to meet demand, quarterly courses have been implemented. As the largest health service in Victoria and a major research hub, Research Platforms were delighted to partner with Austin Health in bringing our free courses in digital tools to them. Medical 3D printing has been used for several research and clinical applications at Austin Health, one of which I’d like to share with you today!Big congratulations to @ozvascdoc and @JasamineCB on the opening of the @3dmedLab! Keep on leading AUS medical! @resplat #3dprinting #3dmed
— Dr. Paul J. Mignone (@PJMignone)
May 26, 2016
#3DSlicer Training @Austin_Health is coming soon! Check your staff email to sign up! #3DMed @ResPlat @3dmedLab pic.twitter.com/3v263fDuT7
— Jasamine Coles-Black (@JasamineCB)
June 6, 2016
Using the Fast March algorithm, Louise and I have shown you in a previous blog post how to quickly isolate regions of vasculature. These vessels can then be made hollow using the Dilate and Subtract Scalar Volumes functions. These hollow, patient-specific representations of arteries and veins have been 3D printed at Austin Health and have been used in patient care, where they give surgeons a better three dimensional representation of the operation that they are about to perform. These 3D models have also been showed to patients, to allow them a better understanding of their disease. These models don’t even necessarily need to be 3D printed- being able to visualise the anatomy from all angles on a tablet or smartphone helps the treating team too!
3D printed abdominal aortic aneurysms such as these have become a mainstay at Austin Health’s 3D Med Lab, with positive feedback from patients and surgeons alike. Surgeons find them a useful aid in difficult cases, although not necessarily in straightforward ones. Some of the feedback that we’ve received from patients is that they prefer being shown 3D personalised models of their anatomy to CTs and MRIs which they have trouble interpreting, allowing them a better understanding of their disease.
Our @3dmedLab @Austin_Health is taking steps in the right direction! #3DMed @ResPlat pic.twitter.com/8pjmb8ny1V
— Jasamine Coles-Black (@JasamineCB)
June 17, 2016
This blog post will form part of a series of case studies where I share my passion for this disruptive technology with you guys. When I’m not making terrible anatomy puns, my consultation hours are Monday morning 10-12 at the CoLab if you’d like to learn how to do this. If you can’t make it then however, feel free to shoot me an email at jasaminecb@gmail.com or a tweet @JasamineCB and we’ll chat then!
We are also running our 3D Slicer for Beginners Course on Monday-Tuesday 4-5th July, 9am-1pm at the Colab, which will equip you with all the basic skills you will need to turn image datasets into 3D surface models. You can find the link to sign up here.
Hope to see you there!
Post by: Rosa Shishegar
Hi All, I’m Rosa!
I am a final year PhD candidate in the University of Melbourne’s Department of Electrical and Electronic Engineering, working in the field of medical imaging. I have recently joined Research Platform Services as a Research Community Coordinator to build a community around medical imaging. Two years ago, the Research Bazaar (ResBaz) community was introduced to me as “a group of computer programming geeks”. Not surprisingly, I found them to be one of the nicest groups of geeks in the university and they helped immensely in solving one of my software issues. So, after more than a month of being stuck in a problem, thanks to them, I could move on with my research.
Let me take you a few years back to the beginning of my journey in medical imaging research. I studied Electrical Engineering (Electronics) in my undergrad. I was intrigued by the idea of studying ‘the Effects of music on brain signals’ to combine my major, Electronics, with my old love, music. I then started a masters in Bioelectronics. In my mind, it was the perfect marriage of my interests and passions. However, at the beginning of my masters and before this relationship could fully bloom, I was introduced to ‘Medical Image Processing’. Ever since I have adhered to medical imaging. I am passionate about the gorgeous, mysterious structures of the brain and all those meaningful colors.
Courtesy: http://www.neuro.uni-jena.de/images/
What do I do with medical imaging?
My PhD research is on brain development. In particular, my research is focused on methods to better understand the process of cortical folding in the fetal sheep brain. As you know the human brain cortex is folded (like a walnut). Understanding the patterns of cortical folding and its mechanism during development is important for early diagnosis of Neurodevelopmental disorders and making improvements in treatments. Why study sheep brains? Because it has easy folding patterns that are similar to the human brain.
Image from: https://au.pinterest.com/oforthesoul/sheep/
In the last few years of my PhD I have developed new methods for processing and the analysis of cerebral cortex structures and morphology using structural MRI and diffusion MRI. The image below is the profile picture of our new Facebook group ‘Medical Imaging @ Unimelb’ that showcases the diverse range of medical imaging applications and analysis tools. I am showing the results from my very own method of assessing the morphology of human brain surfaces (the first three colorful human brains in the top row). Other medical imaging applications highlighted here are visualizing neural tracts (or fancily speaking: tractography), segmentation, 3D modeling, 3D printing and statistical analysis. The tools used to implement these applications include but are not limited to:
Before being a Research
Platforms Community Coordinator, I am a sociable researcher and I enjoy meeting
people and growing in a team. I used to complain that there are not many people
working in my field in the University of Melbourne. The funny part is that
whenever I travel continents for a scientific conference, I meet people who are
working in my field from beautiful city of Melbourne or even from another
department in my own university. I hope with the help of my Research Community
friends Louise, Jas and Warda, we can help the Medical Imaging community in
Melbourne connect more and grow stronger together.
A preview of my recent conference trips!
If you feel you would like to help the growth of this community, or if you are interested in our workshops (all free!), please feel free to join our Facebook group or to contact me rosita.shishegar@unimelb.edu.au, or tweet me at @RShishegar.Hello lovely people!
It is time to meet your new MATLAB Research Community Coordinator (Rescom) – tada!
My name is Warda and I am a data wrangler and a neuroimagineer- yes, this is a thing. In case you are wondering what it means, here is a hint:
A Walt Disney employee card.
Originally posted here: http://tinyurl.com/jsqnygz
I first started coding when I was just over 10 years old. One magical morning in a galaxy far far away, I stumbled upon the deceptively simple looking black hole of GW-BASIC programming environment. I innocently stepped into the world of programming and I have never returned since - I have no regrets :D. Soon after, I found myself fathoming the secrets of algorithm development, syntax, logic and design.
Humble beginnings…
Image courtesy: https://en.wikipedia.org/wiki/GW-BASIC
My experience as a programmer in GW-BASIC led me to the world of C/C++ and very soon I found myself indulging deeply into coding. I became that proverbial coder who is always looking for challenging programming problems and spent hours glued to the computer typing away one line of code after another.
Fire…? What fire…?
Gif credit: http://giphy.com/gifs/13HgwGsXF0aiGY
After completing high school, I started an undergrad degree in Electrical Engineering. In my heart, I knew that C/C++ is the solution to all problems that engineers face and I was confident that I am set to conquer the technical world with the help of my faithful C/C++. However, right after reading the manual of my first ever signals and systems workshop all my confidence came crashing down.
^^ Yes, that is my confidence crashing down!
The thought of implementing convolution of signals and systems in C/C++ sent shivers down my spine and I gaped at the task ahead of me in horror. However, before I lost all hope, I noticed that the manual is instructing me to open ‘MATLAB’! Now here comes a funny bit. ‘Matlab’ is also a word in Urdu, my mother tongue, and it literally translates to ‘meaning’. For a moment, I just sat there, wondering what in the world does this mean and then the awareness dawned when my instructor told me to go to the start menu and open MATLAB! Hallelujah! I must admit that it was love at first sight and I have stayed faithful to MATLAB ever since. Here is why I love MATLAB
Now that I have convinced you the MATLAB was my knight in shining who rescued me from having to write intricate code by presenting me with easily implementable data structures and a treasure chest of built-in functions, let me tell you how MATLAB is still helping me in my pursuit of knowledge.
I am a PhD candidate at Electrical and Electronic Engineering Department of The University of Melbourne. I am part of the Neuroimaging research group in Melbourne Brain Centre. My research is focused on studying movement of water molecules in biological tissue under the influence of extremely high magnetic field for the purpose of characterising tissue morphology. Technically, this area of research is known as ‘Diffusion Magnetic Resonance Imaging (dMRI)’. I spend most of my time analysing and visualising rat brain MRI data in MATLAB, though I am inclined to switch to studying bananas after seeing the MRI image below.
MRI image of a banana - hypnotic!
I found this beauty here: http://giphy.com/gifs/interesting-banana-mri-To3eb1ZkKe7de
I am a data-wrangler at ResBaz and not surprisingly, my favourite tool to teach is MATLAB. Throughout the year, we offer ‘Beginners for MATLAB’ workshops to introduce basic MATLAB concepts to researchers. I am also an admin of our fabulous Facebook group - MATLAB @ Unimelb. This group is a vibrant community of MATLABers for exploring, sharing and connecting online.
Currently, we are in the process of developing extension courses to provide specialised training to researchers with diverse backgrounds. Recently, our champion Rescom, Pippa, beta-tested a fantastic extension course called ‘MATLAB Statistics Toolbox Course’. Rescoms Yamni and Ewan are developing advanced courses for Image Processing and Parallel Computing in MATLAB. As your new Rescom, I am currently developing a ‘MATLAB for MRI’ course with help from amazing cadventurer and fellow Rescom Rosa. This course will focus on importing, visualizing, analysing, 3D modelling and exporting MRI images in MATLAB. If you are an MRI buff and have some cool suggestions for this course, please feel free to ping me (@WardaTaqdees).
Rosa and I have also started a new facebook group ‘Medical Imaging @ Unimelb’ with the aim of providing a platform for sharing, collaborating and discussing various medical imaging modalities. If you are facing a teething coding problem, feel free to come to Colab, hacky hour or PhTea and I will be happy to help. A schedule for my regular consultation hours and our trainings can be found here.
http://melbourne.resbaz.edu.au/calendar
Happy Coding!