Blog awards: April (07/04/16)

The first blog awards for 2016 are here! We’ll be doing these on the first week of every month and recapping our most successful blog posts by our wonderful Research Community Coordinators. 

1. “Before I go, let me tell you a story… “ By Dr. Paul John Michael Mignone
It’s with a heavy heart that we say goodbye to one of our original “first generation” Research Community Coordinators. Paul has been with the ResBaz community from the very beginning & was the lead in kicking off the CADventurer community. A beautiful story by Paul - thank you for everything!

2. “Virtual Surgery using 3D Slicer at the Research Bazaar 2016 Conference” By Louise van der Werff
CADventurer Louise recaps her (hugely) successful 3D Slicer stream at ResBaz 2016! The post contains highlights, recognises the growing community & shares the course notes. 

3. “Autodesk Inventor at ResBaz 2016!” By Aliza Wajih
The CADventurers are on a roll! Aliza’s Autodesk class was majority women (75%) which would definitely make Rosie proud! She recapped the course content and thanked her two wonderful helpers - all in the name of community. 

That concludes our first Blog Awards for April - with the CADventurers out on top! What more can we say but… game on. 

Virtual Surgery using 3D Slicer at the Research Bazaar 2016 Conference

By Louise van der Werff

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.

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.

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.

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.

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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?

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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.

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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. 

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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.

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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. 

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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.

Blog Awards: July/August (20/08/15)

1. “Pop-up Makerspace at the Baillieu” by Fiona Tweedie
Our top story this month was the launch of the UniLibrary & ResPlat collaboration, “Makerspace”! Fiona worked hard to set up a space where students & staff could come together and MAKE - everything from 3D Printing to origami. See the recap here. 

2. “3D Slicer Alpha Training Summary” by Louise van der Werff
Here Louise recaps her training in 3D Slicer - a tool used to analyse and visualise medical scan data. Creating this 3D models can be very useful for teaching and training & even creating custom fit implants and prosthetics! 

3. “#SharksDen Review: Showing researchers another way…” by Paul Mignone
Sharks Den was an innovation project aimed at creating an entrepreneurial community who could turn research ideas into commercial success! Paul, as leader, recounts the idea and implementation process of the immensely successful event! Sharks Den will also be back in our upcoming 3D Printing Showcase (Oct 9&10). 

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.

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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.

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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.

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.

3D Slicer Alpha Training Workshop

by Louise van der Werff

Following my last blog post, I have been busy meeting members of the community and developing training material for the new 3D Slicer workshops soon to be on offer via the Research Bazaar. It’s getting to the point where I would love to share some of this material with the community, but the content and pace of the course is far from polished.

Thus I am on the search for a few willing participants (aka. guinea pigs) to come along and be a part of my alpha training workshop. This workshop will not run smoothly, there will be ‘bugs’, and it will be incomplete. This is an opportunity to gain constructive feedback and guidance from others regarding the content, pace, and length of the workshop.

Image: Volume rendering of a DICOM dataset using 3D Slicer

Below is an 'expression of interest’ form, which you can fill out if you are interested in being part of the alpha training.

Th workshop will be run across three consecutive afternoons (Tuesday the 21st, Wednesday the 22nd and Thursday the 23rd of July) from 3pm - 5pm in the Doug McDonnell building (Level 3) at Melbourne University. All participants are invited to hang around for a drink (coffee/tea/beer/wine) after each session to provide feedback.

There are only a limited number of spots available, and we will try to pick a complimentary team from those who have expressed their interest. I will contact interested parties by Tuesday the 14th of July to let them know if they can attend. If you don’t get picked, don’t worry, a larger, beta training session will be organised soon after.

If you have any questions, please don’t hesitate to contact myself, at louisevanderwerff@gmail.com, David F Flanders at dff.melb@gmail.com

Meet Louise - 3D Modelling Medical Scans!

Hello all,

My name is Louise and I am the newest member of the Research Bazaar team, having just started as a Research Community Coordinator with the team at Research Platform.

After completing a Bachelor of Science and a Bachelor of Engineering (Materials) at Monash University in 2008, I went on to do a PhD in collaboration with Monash University, CSIRO, and Smith & Nephew. During my PhD I developed novel multi-component composite fibres with thermochromic behaviour. In other words, they changed colour with temperature changes (think mood rings in fibre form). Tuned to work in the physiological temperature range, these fibres were created as a potential method for thermal mapping of wounds beds, via their incorporation into bandages.

Later down the track, I was involved in a Researcher in Business program within CSIRO, helping Australian medical devices company Anatomics develop their porous polyethylene surgical implant material PoreStar. Outside of academia I have pursued my own developing interest in 3D printing by purchasing a Makerbot Replicator 2X, combining my knowledge and interest in polymer processing with my passion for DIYing and craft. With this new and exciting piece of hardware I taught myself some rudimentary 3D modelling skills and combined 3D printing with silicone moulding, epoxy resin casting, and general crafty inspiration to come up with some cool new products I now sell online and at markets under the brand name Wordosaurus Text.

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a. my Makerbot replicator 2X, b. a treble clef 3D model in MakerWare c. a silicone mould of the 3D printed master shapes d. A final epoxy resin cast.

I have joined the ResBaz team at Research Platforms to develop awareness and run training sessions relating to medical image processing, in particular the generation of 3D models from medical scan data in the DICOM file format. DICOM image files are produced by a range of medical imaging equipment, (MRI, CT, PET, XRay etc), and consist of a series or stack of cross-sectional image slices across a region of interest in the body. By combining these slices a 3 dimensional representation of the body can be generated.

Generating 3D models of anatomical features from DICOM image files can be beneficial in multiple scenarios. Physical 3D prints of anatomical features such as bones may be used for teaching or training purposes, for the planning of a complex surgery to reduce overall theatre time and risk, and for the creation of implants custom designed and fit to a particular patient. The “3D Printing for Medical Applications” seminar (#3DMed), held on the 14th of April this year, highlighted many applications in which this functionality has been harnessed, and how it could be harnessed in the future.

The software around which the training will be designed is 3D Slicer, an open source community platform with a wide range of capabilities. It’s modular nature provides flexibility and the ability to add on new functionalities as required.  It’s interactive visualisation capabilities includes the ability to display arbitrarily oriented image slices; segment, label features and generate colourmaps, and render 3D models of desired anatomical structures.

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Screenshot taken within 3D Slicer from inbuilt example dataset ‘CTChest’

As this training course is in the very early stages of development, there is ample opportunity for community input and feedback in regards to the content of the material covered. This course is intended to provide researchers and medical staff with valuable and relevant image processing and 3D modelling skills. If you feel you would benefit from this course, or if you know somebody who might, please feel free to contact me to discuss your requirements, at louisevanderwerff@gmail.com, or tweet me at @LouWerff.

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