3DMed Seminar 2016- The Recap

By Jas Coles-Black

The second annual 3DMed Seminar was held on the 5th of October, in conjunction with the 3DMed Lab at Austin Health. The event was hugely successful, with over 130 participants from a whole host of different disciplines signing up to attend. The purpose of the event was to facilitate discussions about the disruptive potential of 3D printing in the medical field, and serve as a catalyst for future ideas and as a meeting point for collaboration!

We were honoured to be joined by a fantastic and diverse list of speakers from variety of different backgrounds. This was in keeping with the #3DMed16 vision of interdisciplinary collaboration, in particular between engineering and medicine, with the shared goal of improving medical research and patient care!

The seminar was kicked out by Dr David Ackland from the University of Melbourne, who took us through a fascinating journey of how he and Prof Peter Lee designed Australia’s first 3D printed titanium jaw, from prototyping to implantation into a patient.

Next up was Dr Eka Moseshvilli from the Olivia Newton John Cancer Wellness and Research Centre, on how 3D printing can be used to create a perfect fit for imperfect anatomy in cancer patients. Her emphasis was on the power of 3D printing to create personalised tools to save lives.

Dr Ian Chao from Austin Health and Box Hill Hospital blew people away with the 3D printed emergency airway trainers that his team had developed, costing less than $2 a model! This has the potential to revolutionise and democratise medical simulation training, with conventional models costing hundreds to thousands of dollars.

We were also treated to a recorded lecture from Dr Steve Pieper from Harvard’s  Surgical Planning Laboratory, on some of the inspiring applications of 3D Slicer worldwide! Some of my favourite examples included utilising 3D Slicer for robotic prostatic biopsies, as well as modelling the morphological and phenotypic changes in various lung cancers.

image
image

 We were also very honoured to have A/Prof Tracie Barber from UNSW come down from Sydney to deliver her talk on using 3D printing in addition to computational fluid dynamics to aid her analysis of blood flow through blood vessels such as fistulas in dialysis patients.

Dr Raf Ratinam from Monash Health explored the views of orthopaedic surgeons on complex 3D printed fractures, and provided a fascinating and instructional overview of how his team were able to achieve these 3D printed models of their patients’ individual fractured bones.

The symposium was finished strong with Dr Ryan Jefferies, curator of the Harry Brookes Allen Museum of Anatomy and Pathology, on how 3D printing was used to enhance the museum’s exhibits, such as a 3D printed recreation of Ned Kelley’s death mask, bringing a 2000-year-old mummy back to life, and a photorealistic 3D printed lung specimen with tuberculosis!

Thank you to all our participants, for your enthusiasm and for providing such engaging discourse both in the panel discussions as well as in the Twittersphere! You helped make this event the success that it was!

Finally, a big shout out to our sponsors, Konica Minolta and Objective3D, for the delicious afternoon tea and for helping to make this event happen!

image
image

In conclusion, we are glad that so many of you found the seminar informative, and most importantly, fun! The feedback we have thus far received has been overwhelmingly positive, and we will without a doubt be holding this event again next year.

If you have any thoughts or feedback about how #3DMed17 can be improved upon, please feel free to email me at jasaminecb@gmail.com, or tweet me @jasaminecb!

We hope to see everyone next year!

Medical 3D Printing Case Study

Post by: Jasamine Coles-Black

@unimelb’s new #3DMed #3DPrinting facilities @UniMelbMDHS @Austin_Health pic.twitter.com/s9yo03tHYC

— Jason C (@ozvascdoc) May 17, 2016 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!

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!

image
image

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.

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!

3D Slicer at the Victorian Institute of Forensic Medicine

Post by Jasamine Coles-Black and Louise van der Werff

Recently we ran two 3D Slicer for Beginners workshops at the Victorian Institute of Forensic Medicine (VIFM) in Southbank. This opportunity was organised by Andrea Hince, Communications Manager at VIFM, who also helped to facilitate Paul Mignones visit to VIFM last year, and was conceived after speaking with Forensic Egyptologist Dr Janet Davey, who is interested in exploring ways of generating 3 dimensional models from the CT scans of mummys, particularly children.

Attendees were predominantly staff at VIFM, with backgrounds including but not limited to Clinical Forensic Pathology, Forensic Medicine, Forensic Training and Development, Forensic Radiology, Forensic Communications, Forensic Mortuary Science, Forensic Anthropology and more.

As with previous workshops, we predominantly focussed on segmenting anatomical features from medical image datasets such as MRI and CT scans, and generating 3D models of those features, which can then be viewed and interacted with virtually or 3D printed into a physical object. Most participants were unfamiliar with 3D Slicer and were interested in better grasping the potential of 3D modelling and 3D printing as a tool (e.g. educational, investigational) in the clinical forensic domain. Of particular interest was 3D Slicer’s ability to visualise and extract anatomical information from CT scans.

Some potential reasons presented for this capability in forensics include being able to demonstrate anatomical features and structures in the courtroom (e.g. by producing 3D models for court demonstrations), for Medico-legal death investigations, for teaching and training purposes, and historical forensic investigations.

Dr Chris O’Donnell, who participated in the first workshop in April, spoke about 3D printing in forensics during last years 3D Printing for Medical Applications Seminar, held at Carlton Connect. You can watch his talk “Use of 3D prints in medico-legal death investigation” here. Chris O’Donnell and his team scans thousands of diseased bodies each year, as a way of looking into a body without having to conduct an autopsy (or in addition to an autopsy), and in cases where deaths are unexpected or suspicious, or when identities are unknown. The collected data can be used as evidence in court, presented not to medical professionals but to lay public such as defendants, judges, jury members and lawyers, and as such, clarity of that information is very important. The generation of 3 dimensional virtual representations of anatomy can greatly assist in conveying medical concepts, and 3D printed specimens are seen as another valuable addition to the evidence. Examples presented include a large volume haemopericardium, lacerations to a kidney, and fatal skull fractures.

In addition, medical image processing has been used in the forensic literature with great effect. In one case report, the victim’s skull was segmented from an antemortem CT scan in order to successfully identity the murder weapon via virtual modelling of the skull, as well as comparing a 3D printed replica of the victim’s skull to the matching weapon. (1) These techniques were used to circumvent the obstacles created by medical intervention and the healing process.

Image source

In another similar case of blunt trauma to the skull, a major benefit cited by the group was the ability to maintain the dignity of the victim while still providing an excellent 3D representation of the deceased’s anatomical structures and injuries for presentations in the courtroom. (2)

During the recent courses we have run at VIFM, we have instructed our participants in how to use 3D Slicer to generate similar skull models from medical imaging, as pictured below. The skull was automatically segmented from the surrounding tissue using first principles - in this case, the difference in Hounsfield units, or relative radiodensity, of the dense skull bones compared to the surrounding less dense soft tissue, was used to separate the two.

Image source

If you feel like you’ve missed out, fear not! This content was not a VIFM exclusive. If you would like to learn how to do this, feel free to sign up for our next 3D Slicer for Beginners course and we’d love to show you how!

Automatic segmentation of a skull using the thresholding tool in 3D Slicer. Come along to our next course if you’d like to learn how to do this!

Our next 3D Slicer For Beginners course will be on the 4-5th July, 9am-1pm both days, at the CoLab, Old Quad (G08). Sign up here, and we’ll catch you there!

  1. Woźniak K, Rzepecka-Woźniak E, Moskała A, Pohl J, Latacz K, Dybała B. Weapon identification using antemortem computed tomography with virtual 3D and rapid prototype modeling—A report in a case of blunt force head injury. Forensic Science International. 2012;222(1-3):e29-e32.
  2. Kettner M, Schmidt P, Potente S, Ramsthaler F, Schrodt M. Reverse Engineering-Rapid Prototyping of the Skull in Forensic Trauma Analysis. Journal of Forensic Sciences. 2011;56(4):1015-1017.

Before I go, let me tell you a story…

By Dr. Paul John Michael Mignone

It was late 2013, and I was invited to David Flanders’ house to discuss this new ‘researcher training initiative’ that ITS Research (now known as Research Platforms) was starting. I had met David the year before at a 3D Printing build party, and had helped him run a University-wide build party in early 2013. Aside from being one of the coolest, most dynamic people I had ever met, David had (and continues to have) the fantastic vision of building a community of researchers that were proficient in data science tools, and were able support researchers to do better quality, reproducible research.

image

In The Beginning: The Pre-ResBaz 3D Printing Build Party!

At this point in time, I was at an ‘interesting’ stage in my PhD/life (same thing back then ;-). My PhD was facing some difficulties (to put it mildly), and I was running out of funding. At the same time, I was trying to setup my own initiative to get CAD training integrated into the engineering curriculum at Unimelb (with little success). Having been in the private sector before returning to academia, I felt the engineering students at Unimelb were at a disadvantage by not having basic CAD skills, especially in a tough job market where employers can be ‘picky’ with candidates.

image

PhD: Mission Accomplished!

Therefore it shouldn’t be a surprise to anyone that I said YES when David offered me the job to teach CAD as part of this ‘Research Bazaar’ initiative. For me it was an opportunity to teach engineering students and researchers relevant technical skills, while earning some money to finish my PhD (and cover my mortgage!). Back then we started with only six people: Me, Dejan, Steve, Damien, Katie and Grischa. Nearly three years later, I honestly did not expect to see ResBaz where it is now.

image

What did ResBaz achieve in under 3 years? Look above…

The journey I’ve shared with ResBaz has been incredibly exciting and highly rewarding. I no longer see CAD as a tool for just designing and 3D printing ‘stuff’, but as a tool to create, manipulate and enrich 3D data. For me, CAD is a tool that is part of the great chain that is data science, and has the potential to be used far more effectively when combined with a dedicated research community, and other data science tools. As ResBaz grew in size (about 30 staff today), I had the opportunity to develop new professional skills by mentoring, leading and managing a team of brilliant individuals (Aliza, Louise and Vincent) under the #Cadventure stream. Today this team, now under the leadership of Dr. Louise Van Der Werff provides community, expertise and training around tools that create, manipulate and enrich 3D data.

image

#Cadventure: An amazing team to lead!

ResBaz also provided me with the opportunity to work with a phenomenal group of people. People that were friendly, hard working, frighteningly talented and incredibly passionate about data science tools and their fields of research. A group of people that I count among my good friends today. As I head off overseas to do a postdoc, I realised that very few us in our careers will get the opportunity to work for an organisation where you get to build something from scratch. Something that you’re passionate about, and something that will change the way things are done for the better. To have the opportunity to build #Cadventure at ResBaz was a privilege, and something I will never forget. I would like to thank David, Steven, Nicole and all of the Research Platforms staff (current and former) for making ResBaz the amazing organisation it is today.

image

#ResBaz: A phenomenal group of people!

For those interested in seeing my ResBaz story in the blogosphere, you can catch my work here: http://melbourne.resbaz.edu.au/tagged/paul 

If you would like to stay in touch, you can reach me on twitter or my new blog, where I will continue my outreach efforts: https://paulmignone.wordpress.com

As I set towards Ithaca once again, I thank the entire ResBaz community for an amazing adventure :-)

This is Dr. Paul John Michael Mignone, signing off…

image

Upcoming 3D Slicer Workshop

By: Louise van der Werff

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. 

image

3D Slicer at the Research Bazaar conference, 2016

From ResBaz to ResBaz: A Glorious Year for 3D Data!

By Paul Mignone

image

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:

  • At ResBaz 2015, I successfully launched a pilot initiative in partnership with Nvidia for students to access graphically intensive CAD software in the cloud. The pilot was highly successful, and has given Research Platform Services valuable information for future ‘Cad in the Cloud’ rollouts in 2016 and beyond.
  • Our most recent hire, Vincent Khau, is now our resident 3D printing and lightweight CAD guru, offering courses in TinkerCAD and Autodesk Fusion 360. Vincent has been hugely successful in engaging Unimelb’s Victorian College of the Arts, offering regular lightweight CAD courses at VCA, as well as engaging them in various research projects.
  • Due to the huge demand and interest in 3D printing over the last few years, The University of Melbourne’s 3D printing showcase was held for the third time at Wilson’s Hall. The massive building was barely large enough for the huge turnout at the 3D printing showcase, which saw over 3000 attendees over a single weekend.  The showcase displayed the latest 3D printing technology, race car challenges, hackathons, community makerspaces, as well as lives lectures and interviews.
image

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:

  • Aliza and her helpers successfully ran the Autodesk Inventor stream, which is now a community 400% bigger in size, and with far greater gender representation.
  • The ResBaz Partnership with Carlton Connect continues to grow in 2016. We now have a residence at their Lab-14 innovation precinct, and plan to run more joint events in the near future. Carlton Connect also made an appearance at ResBaz 2016, advising researchers on avenues to commercialise their research.

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!

image

We are part of something bigger…

3D Printing at Austin Health

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.

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!

3D Slicer Workshop Recap!

Below is a recap of the recent 3D Slicer training workshop. 

If you are interested in attending a 3D Slicer workshop, the next one will be held as part of the Research Bazaar 2016 conference, a free 3-day intensive event (Feb 1-3rd 2016) for researchers at all stages in their careers (Honours, Masters, PhD, Post-Docs, ECRs and so on) to engage with the wider community and learn new digital research skills.

Simply follow the links below to sign up and select 3D Slicer as your first preference from the available teaching streams. This conference will be an amazing experience for all, and will include a great range of social activities, fun and games.

Have a question? Check out our FAQ: melbourne.resbaz.edu.au/resbaz2016. Apply at resbaz.com/melbourne.

—————————————————————————————————-

The 3rd ever 3D Slicer for Beginners workshop was held at Melbourne University last week. 15 enthusiastic participants, one lovely Helper, and a guest appearance from Objective 3D made this workshop both interesting and informative. This workshop the very recently released version 4.5 of 3D Slicer.

For me, this workshop was my most intimidating. The turnout was double that of the previous workshop I held in August, and triple that of my very first workshop in July. This increasing turnout shows increasing awareness and interest in this kind of software around Melbourne University and beyond.

Participants came from a range of academic backgrounds, including Anatomy and Neuroscience, Agriculture and Veterinary Sciences, Electrical and Electronic Engineering, Nanofabrication, Psychology, Physiotherapy, and even video game design.

Jasamine Coles-Black, an MD research student in vascular surgery at Austin Health, kindly volunteered to be a helper at my workshop, after having attended the previous two 3D Slicer workshops.

Ben Darling, the National Sales Manager for Objective 3D, kindly offered to bring along some 3D printed anatomical objects to show off some of the abilities of advanced 3D printers like the Connex 3, which offers multi-material printing, “from rubber to rigid, transparent to opaque, neutral to vibrantly colored and standard to biocompatible.”

For the majority of the workshop, participants were taught the steps required to generate 3D surface models of anatomical features from DICOM datasets such as MRI and CT scans, for 3D printing and visualisation purposes.

image

Image: A 3D volume rendering of a brain that has been isolated from an MRI scan of a patients head. 

Feedback from the workshop was very positive. The below interactive graph displays the score out of 5 that participants (who filled out the end-of-workshop survey) gave for a number of different questions. 

The majority of participants felt that the material covered in the workshop was relevant to their research/interests, and many of them intend to continue using 3D Slicer in the future. 

If you have any questions or comments, don’t hesitate to contact me.  You can email me at louisevanderwerff@gmail.com and tweet me @LouWerff.

Using Digital Skills and 3D Printing to Create  Wound Simulation Models for Austin Health

By Louise van der Werff and Jasamine Coles-Black

What do you get when you combine Autodesk Inventor, Meshmixer, 3D printing, Lego blocks and silicone moulding? A wound simulation model for nursing students at Austin Health! The following post outlines the step by step process we used to generate a viable research/training product using digital CAD tools for the medical community.

A couple of months ago Paul Mignone and I (Louise), along with Dr Jason Chuen and Jasamine Coles-Black collaborated to create a new training product for the Austin Hospital Clinical Skills Simulation Laboratory. They wanted to create models to simulate a wound or ulcer that extended under the skin, and use those models for nurses during training sessions to practice washing and irrigating a wound cavity, before packing it with gauze.

Prior to the creation of these new moulds, the Simulation Laboratory was using a variety of other models when running their training sessions. However, there was no uniformity in the models used and some did not have a cavity deep enough to be packed with gauze. In addition, some of the previous models were made of polyurethane foam, which, after the addition of Thai sweet chilli sauce as mock “blood”, resulted in perpetually sticky models as they could not be easily cleaned.

image

Image: A previously used wound simulation model, made from painted polyurethane foam.

The brief was that the model needed to be waterproof and washable, reusable, and the wound cavity had to be irregular, and have an overhang of ‘skin’. They also wanted 10 identical models, so generating these models in a reproducible and cost effective manner was quite important.

After some consideration we decided to use a soft silicone rubber as the model material. All we had to do was create a negative impression of the wound cavity, and cast silicone rubber around it to create the final model.

I was able to use some of the 3D modelling skills I had learnt in the Research Bazaar Autodesk Inventor course run by Paul Mignone and Aliza Wajih to prototype the wound model using the following steps:

I created an underlying flesh layer, and ‘scooped out’ a cavity using sketch, extrude (cut) and bevel tools. I then created a skin layer, which extended past the boundary of the wound bed to create an overhang. Last but not least, I created a new object which represented the negative of the resultant wound cavity. Pretty cool huh?

image

Image: Forming the ‘flesh’ and ‘skin layers in Autodesk Inventor.

Since wounds aren’t generally nice and smooth like engineering shapes, I exported this resultant 3D shape into MeshMixer, and used its 3D sculpting tools to add a little bit of unevenness to the model.

image

Image: MeshMixer sculpting before and after.

I then printed the shape out on a Makerbot Replicator 2X in ABS plastic, used sandpaper to smooth the surface just a little, and I was ready for silicone casting!

The 3D printed shape was glued upside down onto a flat surface. I then used Lego blocks (highly versatile!) to build up a ‘container’ around the shape to contain the silicone. To make the moulds I used Pinkysil, a very easy to use cast-able bright pink silicone which cures quickly and is relatively soft. 

image

Image: Before and after pouring Pinkysil silicone into the mould container.

After curing, the 3D printed negative was pulled out from the silicone, leaving an impression, which became the simulation wound bed! The ease of this process meant I was able to make 10 identical models relatively quickly.

image

Image: Close-up of a single resultant wound model, and the 10 identical models.

The models have already been used in a training workshop for second year nursing students, with very positive feedback. The students loved them, they were an enjoyable teaching tool, and a great improvement to previous models. They were also easy to clean (they could simply be rinsed off and put away at the end of the session), and having 10 models in a session meant each student could follow through the steps at the same time, rather than having to rotate. 

image

Image: The wound models, stuffed with irregular wound material for simulation training.

If you have any questions at all about this process, please don’t hesitate to get in touch. You can email me at louisevanderwerff@gmail.com and tweet me @LouWerff.

New 3D Slicer Workshop Announcement and an Engineering Application!

By: Louise van der Werff

Hello all! The next 3D Slicer workshop is scheduled to run across two afternoons on the 24th and 25th of November. Sign up to participate for free here!

Check out my previous blog posts here and here to see how 3D Slicer can be used to generate 3D models of anatomical features from medical scan data. The recent 3D Printing Showcase held at Melbourne University had some fantastic 3D printed anatomy displays, hopefully some of you were able to come along and gain some inspiration!

I thought I’d supplement this blog post with another example of how 3D Slicer may be used, not in the medical field however, but in the engineering field.

Although 3D Slicer is targeted towards the processing and visualisation of medical scan data, it’s applications aren’t necessarily limited to medical applications. At its core, 3D Slicer is all about image processing, regardless of where those images came from, and although much of the image data 3D Slicer will process comes from DICOM datasets, other sources can be imported just as readily.

I was given an image stack consisting of 99 2 dimensional images (in .tiff file format), of an alumina foam micro-structure. This dataset was created using micro-computed tomography (MCT) and can be used to generate a 3 dimensional representation of the alumina foam structure.

image

Image: The alumina foam samples, and micro-structure as captured by micro-computed tomography (MCT).

When importing these images into 3D Slicer, they are combined into a volume, and I was immediately able to view the dataset not just in the direction that the images were captured in (z axis) but along the x and y axis. A 3D volume rendering of the composite could also be readily generated.

image

Image:  The alumina foam viewed in 3 perpendicular directions, and a 3D volume rendering of the dataset.

3D Slicer comes with hundreds of basic and advanced image filters from ITK. The Median Image Filter reduces noise in an image while preserving image edges, by replacing the intensity of each pixel with the median intensity of surrounding pixels. This makes subsequent image segmentation (labelling different sample features with different coloured labelmaps) easier. The below image series shows the sample image being filtered, then segmented into two regions, representing the alumina (green) and empty pores (red). A fairly good binary representation of the micro-structure is quickly achieved.

image

Image: The alumina foam micro-structure filtered, then segmented into two labelmaps.

These labelmaps can then be used to generate a 3D surface model of the two regions, as shown below, which may be visualised virtually, or 3D printed into a physical object.

image

Image: 3D surface models of the alumina foam, representing the alumina (green) and pores (red).

So, in essence, even if you aren’t in the medical field, you may find 3D Slicer useful for an entirely different purpose!

For more information, feel free to contact me at louisevanderwerff@gmail.com, or tweet me @LouWerff.

#HealthHack Science Day at the MCRI

By Louise van der Werff

Last week a tour was conducted through the facilities at the Murdoch Childrens Research Institute (MCRI), and I was happily invited to tag along as a representative of our little team at the Research Bazaar! The tour was organised by Dr Marguerite Evans-Galea (Maggie), a scientist specialising in neurogenetic diseases, for the winning team members of #HealthHack 2014, an initiative connecting medical researchers with software engineers to solve research problems.

The tour was focussed around some of the facilities and people involved in genetic disorder research, genome sequencing and gene therapies, a fascinating and highly complex field. Identifying genes responsible for genetic disorders and developing targeted treatments for those disorders is a mammoth task, but it looks like they have it well in hand.

The first port of call was the Translational Genomics Facility (a facility within the collaborative Melbourne Genomics Alliance), which holds some very impressive next-generation DNA sequencing equipment. The HiSeq 4000, worth a cool $1.8 million dollars, can carry out a full genomic sequence of up to 6 genetic samples in less than 3.5 days using a patterned flow cell technology, and outputs a whopping 4TB of data per run! They must have some hefty data storage capabilities at the MCRI! If not, they can always talk to Data Services here at Research Platforms Services :)

image

Image: Dr Stefanie Eggers showing off the HiSeq 4000.

We were then treated to a presentation by George Charalambous from Curve Tomorrow, a six year old innovation company that has a digital health partnership with MCRI. Their mission? To create products that have a positive impact on society. Amongst other things, the team look at harnessing established technologies such as Microsoft Kinect, Google Glass and Oculus Rift for medical applications that involve motion tracking, and for simulation training (such as CPR training). They have also developed a number of iPad apps, including P.E.E.R.S (Pediatric Evaluation of Emotion, Relationships and Socialisation), which can be used by clinicians to diagnose and evaluate autism in young children, by, for example, testing their ability to match a written emotion to a facial expression in a relaxed, gamified way.

image
image

Images: The PEERS iPad app, and a wristband that tracks muscle twitches.

Next up was Dean Phelan, a PhD candidate studying novel genes associated with cardiomyopathy. Dean is looking at methods of identifying causal genes by reprogramming patient skin cells into induced pluripotent stem cells (iPS cells) and then differentiating them into specialised heart cells for disease modelling and drug treatment screening. Did you know that differentiated heart cells start beating together spontaneously in a petri dish? I didn’t either! Luckily enough we got to take a look through an optical microscope in the cardiomyopathy lab to see for ourselves.

image

Image:  Dean Phelan with his Petri Dish loving differentiated heart cells.

One of Dr Maggie Galea’s PhD candidates, Sze Hwee Ong, gave us a great overview of her research looking into cell and gene therapy treatments for Friedreich ataxia, a neurodegenerative disease that causes progressive damage to the nervous system. 

In the BLC (Bruce Lefroy Centre) Lab, we met Greta Gillies, who showed us her technique for extracting DNA out of blood samples for further analysis. It was surprisingly similar in principle to the strawberry DNA extraction experiment I remember doing as a kid. We also saw some of the freezers used  for the long term storage of tissue and blood samples, and were introduced to the concept of immortalising cell lines.

image

Image: Greta Gillies speaking to the tour group in the BLC lab. 

And last but not least we met Kate Pope, a registered nurse and Associate Genetic Counsellor. She has the weighty task of working with kids with genetic disorders and their families, providing them with information and getting their consent for exploratory procedures aimed at identifying the genes responsible for their disorders, such as epilepsy. This may involve taking skin and even brain tissue samples for analysis and genetic sequencing. Dr Maggie Evans-Galea spoke of the powerful moments when Kate is able to make a phone call and break the news that the responsible gene has been identified, allowing for better and more targeted treatments for the patient.

All in all it was a fantastic and eye opening experience, but I feel we only really touched the surface of what goes on at the Murdoch Children’s Research Institute.

If you would like to learn more, Dr Marguerite Evans-Galea can be contacted via marguerite.galea@mcri.edu.au and tweeted at @MVEG001

The Benefits of 3D Printing Anatomy and 3D Slicer Training

By: Louise van der Werff

Another 3D Slicer training workshop has been set! Running across two consecutive afternoons on the 25th and 26th of August, this workshop follows on from the alpha training workshop in late July, which you can read more about in my last blog post.

Registrations can be made for the new workshop via Eventbrite here.

A couple of months ago I had the pleasure of attending a seminar by Professor Paul McMenamin, who is the Director of the Centre for Human Anatomy Education at Monash University. The talk, titled “Innovations In Replication of Human Anatomical Dissections by 3D Printing: uses in Education and Research”, discussed ways in which the use of 3D printed bio-models for teaching and training purposes could replace more expensive and less accessible methods such as the use of cadavers and plastinates (diseased human bodies).

Obviously exposure to real human anatomy is a great way for medical students to learn. However, the cost of accessing cadavers can be in the thousands of dollars, and further preservation techniques such as plastination (a technique used to preserve a whole body or parts of the body by removing water and fat and replacing them with certain plastics) requires specialised labs, licenses and materials, and can add tens of thousands of dollars more onto the cost.

image

Image: A plastinate of a horses hoof. Photo by Dr. Christoph von Horst (own work; http://www.plastinate.com) via Wikimedia Commons.

Coupled with the strict ethical considerations involved, real human bodies are not an ideal or necessary medium for all teaching situations. 

One alternative to the use of cadavers and plastinates for teaching purposes are stylised plastic models. These can be cheap, but are often not very realistic.

Paul and his team have come up with an alternative: 3D modelling and printing real human anatomy. CT scans of human anatomy are used to generate highly realistic 3 dimensional digital models, which are digitally coloured to distinguish different anatomical features, before being 3D printed (in colour!). For comparison, a plastinate of an arm might cost $14,000, while a 3D printed equivalent model can be produced at around the $100 mark. Couple this with the fact that a large number of live patients can be used as models for comparative purposes, multiple copies of the same model may be generated easily, and at a range of different scales, it is an attractive alternative for anatomy education. 

Pictured below is a 3D colour printed model of the blood vessels in a human skull, a structure that would be very difficult to produce any other way.

image

Image: A 3D printed anatomical model displayed at the seminar.

Cells and other microscopic structures may also be modelled and printed relatively easily.

All in all, it was a fascinating look into the ways 3D printing technologies may be harnessed in the medical field. 

For more information about anatomical 3D printing at Monash, follow this link. 

If you would like more information about the 3D Slicer training, or have any other questions, please contact me at louisevanderwerff@gmail.com.

#SharksDen Review: Showing researchers another way…

by Paul Mignone

It is considered tradition when submitting a PhD to provide a quote to sum up your research journey. On submitting my PhD a couple of months back, I used the following quote to summarise my nearly five year journey of discovery (and drama).

“One of the best lessons children learn through video games is standing still will get them killed quicker than anything else.”

- Jinx Milea

From working in engineering (both internationally and locally), to having my own business, pursuing a materials engineering PhD and working with Resbaz, Jinx’s words sum up my last ten years perfectly. In short, I haven’t stopped moving in my career. I’ve pursued new and interesting experiences that have made me both a better engineer and person. More importantly, these experiences have given me the skills and inspiration required to address the challenges facing Australian researchers today.

The inspiration for #SharksDen…

It is no secret that the current landscape for research (and research funding) is challenging for Australian researchers. Government expenditure on science and research in Australia (as a proportion of GDP) has fallen by more than a quarter since 1993. In addition, a recent National Tertiary Education Union (NTEU) survey showed that only 17% of Australian researchers have ongoing employment. This challenge is even greater for early career researchers (ECRs), with the chance of securing an ARC grant for early career researchers (known as a DECRA) sitting at approximately 10%.

In such a competitive environment, ECRs will need to find new and innovative ways to secure research funding (e.g., private endowment, startup grants, Thinkable.org etc.). They’ll also need skills, training and an innovation community to adapt their research and skills in more commercial ways. In short, we need early career researchers to be a little more ‘Shark’, constantly moving and adapting to Australia’s research funding challenges.


Cue in #SharksDen… 

While the Research Bazaar has had many successes building research communities around programming languages, CAD and 3D Printing, I’m passionate about engaging researchers in a way where my skills and experiences in the private sector could be used to help them ‘future-proof’ their working careers. With the help of my (awesome) boss, David Flanders, ResBaz has created an innovation community for researchers, helping them find ways of ‘translating’ their research into valuable commercial products and services.

The #SharksDen is an innovation training program which brings early career researchers together with students, professional staff, entrepreneurs and private sector employees. Over five evenings spread out over the month of July, participants in the program did the following:

Day 1 - Team formation and idea generation techniques (Day 1 summary).

Day 2 - Learning 3D modelling and design with TinkerCAD (Day 2 summary).

Day 3 - Learning how to use 3D printers (Day 3 summary).

Day 4 - How to pitch for startup funding (Day 4 summary).

Day 5 - Teams presented their products to a professional panel (Day 5 summary).

The #SharksDen presentation evening at Carlton Connect…

By the time of the #SharksDen presentation evening had arrived on July 29th, there were four teams ready to pitch their innovative products to the panel:

  1. Artistic Instrument Designing Co., presenting their bespoke guitar components.
  2. Next Gen Cover, presenting their next generation, multi-function phone cases.
  3. Radiance, presenting their low-cost bike light.
  4. Fit’n’Click, presenting their bespoke computer mouse for esports and other emerging industries. 

The panel brought together a blend of experience in startups, 3D printing and 3D modelling, which consisted of the following members:

Mr. Rohan Workman: Director of the Melbourne Accelerator Program.

Mr. Matthew McKnight: Senior Technical and Design Specialist for Autodesk.

Ms. Grace Carey: Managing Director at Gynaecologic Pty Ltd.

Mr. Dinesh Kantheti: Designer of 3D printers and founder of 3inter.

A massive shout out to all four members for volunteering their time to be on the panel! Each team presented a four minute pitch to the panel, articulating the benefit and profitability of their products in the market. While competition was very tight, the winner was determined to be Fit’n’Click with their customised mouse design. A special mention goes out to the runner-up team, Radiance, for getting a working prototype up and running in only four weeks! A special thank also you to goes out Marcella, Dejan and Nicole for handling the media and catering at the #SharksDen presentation evening.

What the #SharksDen researchers say…

Despite being a voluntary program we were amazed how all four teams worked hard and passionately together to produce their final products. The quality of their designs and pitch presentations were well above our original expectations (a big shout out to Gil and Wen for helping out at the classes!).

Since the event, attendees (and teams) have expressed interest in working on their products further, with some planning to apply for the Melbourne Accelerator Program in 2016. The researchers who participated in #SharksDen also felt that their new skills and experiences would help them in their working careers.

Gene Venables, a research officer at the University of Melbourne said the following (link to the full guest article):

“It has changed the way I think about products I use, and I’m sure it will influence ideas that I conceive in the future…Over the five weeks I worked with a group of talented people from a variety of different backgrounds. I hope to foster further collaborations and I am excited to venture into deeper water with my new skills.”

Khalid Abdulla, a PhD candidate at the University of Melbourne said the following (link to the full guest article):

“I feel that I have learned a lot from taking part in the challenge. In particular the different roles which need to be filled in a small startup company, the different requirements which need to be satisfied for a product to be novel and successful, and finally the importance of, and some handy hints for pitching. As a researcher it’s important to remember that doing the research is only part of the job, it is also necessary to communicate/sell the research, and I think the “pitching” training was useful for developing those skills. Most importantly…it was fun.”

What next for #SharksDen?

The next #SharksDen is planned to run during the 2015 3D Printing Showcase on October 9th-10th.

Stay tuned for details!

#SharksDen: A Researcher’s Perspective (Part 1)

by Gene Venables

Entering into the Shark’s Den from the research world I didn’t quite know what to expect. My hopes were to meet new people and to build my very rudimentary 3D modelling skills. As a researcher I had dabbled with 3D printing technology to make some simple equipment to help my lab work. But they were just one-off pieces for my own use and sense of accomplishment.

In the Shark’s Den I learned of a world which I hadn’t considered previously. Commercialisation; and how others are interested in my using the pieces I’ve made. By the end of the intense five week programme I pitched an idea I was proud of, and thankfully I didn’t completely flounder in my first pitch. I found the Shark’s Den to be a great way to just dip my toes in, and learn about how the incubator and start-up world works.

I hadn’t considered it beforehand, but I came to realise that so many products in the modern world that I use, from the watch on my wrist to the smart phone in my pocket (and many the apps on it!) had gone through this pitch process. It has changed the way I think about products I use, and I’m sure it will influence ideas that I conceive in the future.

The programme was well instructed and guided throughout, and I never felt lost at sea. Over the five weeks I worked with a group of talented people from a variety of different backgrounds. I hope to foster further collaborations and I am excited to venture into deeper water with my new skills.

Gene Venables
Research Support Officer
Anatomy and Neuroscience
The University of Melbourne

3D Slicer Alpha Training Summary

By Louise van der Werff

Last week I ran my newly developed 3D Slicer training workshop over three content-packed afternoons. Five willing participants were able to come along and get their first peek at the training material, provide very helpful feedback related to the structure of the workshop, and brainstorm ways in which this software may be harnessed in their own work.

For those who may not be familiar with 3D Slicer, it is an open source software package for image visualisation and analysis. More specifically, 3D Slicer is tailored towards the analysis of medical scan data such as that generated via MRI and CT scans. Although 3D Slicer has a wide range of functionalities, this workshop was primarily focussed on generating 3 dimensional volume renderings and surface models of anatomical features from medical scan data.

After giving an introduction on the principles of image processing, I conducted a tour of the 3D Slicer graphical interface, then gave the participants a series of challenges to generate 3D surface models of different anatomical features.

The first step towards generating a 3D model involves image segmentation, which is the process of separating an image into distinct components to make it more meaningful for software to analyse. This is done by assigning each pixel belonging to a particular object a label.

Segmentation of a photo into three distinct components. 

Anatomical structures are segmented from medical scan datasets in 3D Slicer by generating a labelmap over the feature of interest. Anatomical structures we segmented during the workshop included bone, lungs, airways, lateral ventricles, and a trachea and larynx. We explored both manual and automated segmentation methods, their appropriateness being predominantly dependent on the level of contrast between the feature of interest and the surrounding volume.

A particularly challenging case was manually segmenting the trachea and larynx from an MRI scan. Below is a picture of the original scan data, the segmented labelmap, the generated 3D model, and a 3D print of the model to-scale.

An MRI scan of a child’s trachea and larynx. These were manually segmented before a 3D surface model was generated and then 3D printed to scale. 

In addition to segmentation, we also touched upon basic image registration, adding annotations such as fiducials and rulers to a dataset, using statistical tools to calculate volumes of segmented regions, and creating scene views.

The generation of 3D models of anatomical features may be beneficial to many researchers and clinicians, for teaching and training purposes, surgical planning, the creation of custom fit implants and prosthetics, and simple visualisation.

As well as using local installs of 3D Slicer on laptops, we are also currently exploring the effectiveness of running 3D Slicer from the NeCTAR Research Cloud via resbaz.cloud.edu.au (which is powered by the DIT4C engine). A couple of participants tried this approach out with promising results. One major benefit of running graphically intensive software from the cloud is that performance is not limited to the specifications of  local devices, and resources can be scaled as required.

Major points of feedback from this alpha 3D Slicer workshop was that participants preferred more practical content to theory, and wanted to get hands-on with the software as quickly as possible. It was great to see ideas flowing near the end of the workshop from participants about how they might apply 3D Slicers functionalities to their own research projects. Some participants were also interested in exploring whether 3D Slicer could be applied to non-medical applications, such as in the Materials Engineering field.

The alpha training material can be viewed and commented on here.

Please keep an eye out for more training sessions, soon to be announced! If you have any questions, please don’t helistate to contact me at louisevanderwerff@gmail.com or tweet me @LouWerff.

Top