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.

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 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!

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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!

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.

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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.

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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.

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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.

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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.

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.

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