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. 

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3D Slicer at the Research Bazaar conference, 2016

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.

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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.

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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.

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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.

You’re a data vizard, Harry!

by Isabell Kiral-Kornek

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“A data vizard!”

“No, you made a mistake! I can’t be a data vizard! I’m just.. a researcher!“

“Have you ever thought about making your data accessible to the world, open for everyone to see, using another dimension to add interactivity?”

We’ve written, prototyped, tested, revised, and now we’re finally ready to turn you into a data vizard, too! 

After a successful alpha-training earlier this year (massive thanks to our wonderful helper Harriet!) and a trial run at CERN, we’re running our first full workshop in Melbourne, starting on 30/11.

Come along, learn everything from setting up a simple website to host your data to making it look stunning using D3js! 

More info and sign up here!

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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.

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.

Vincent talks #SharksDen: Day 3

by Vincent Khau

Day 3 of Shark’s Den meant we were already at the halfway mark of this exciting innovation challenge yet it only seemed like yesterday that we had met our fellow team members. We were now rapidly approaching the pointy end of things and ideas were flying out left right and centre as teams worked together to produce a marketable product.

The first hour flew by as each team quickly discussed the prototype designs that they were going to 3D print, before the CTOs were whisked away by Paul and given a tour of UniMelb’s 3D printing facilities, along with a demonstration of how they worked. Everyone was palpably excited as they learnt about both the advantages and (present) limitations of this fascinating additive manufacturing process. During this time, the remaining team pooled their minds together and increased their efforts to further refine and reiterate on their existing product, now calculating and ironing out the technical details of design, trying to bring the product to life; out from the confines of their minds and into the real world.

The teams were fortunate enough to have the expertise of Gil who came along to give advice to each team on their product, getting them started on not only thinking about the current design, but future considerations of the growth and development of their product.

As the end of the session approached, the teams rushed to get their models off to the 3D printers. This acted merely a starting point from which they need to produce rapid reiterations to get their product ready for their pitch on the 29th of July.

Beginner’s MATLAB Workshop for Researchers

BACK BY POPULAR DEMAND! 

Due to the huge success of the female oriented workshop that we ran in May this year, we are proud to announce that we’ll be holding a beginner’s workshop, open to all researchers. 

MATLAB is one of the standard tools in science & engineering. It is an extremely versatile high-level programming language that allows you to do pretty much anything: from controlling hardware to recording, analysing, and visualising data. And the best thing is that you can test small parts of your program immediately.

During the workshop, you will get a basic introduction to MATLAB’s user interface and then learn about basic programming concepts that allow you to write programs to read in and analyse your own data.We will cover how to write and use scripts, loops, functions, and conditionals. 

Know your way around MATLAB, or want to refresh what you learnt last time? Then contact us to join our awesome team of helpers.

Find a more detailed explanation, dates, and schedule here and make sure to sign up! (This workshop is limited to 30 attendees.)

See you there!

MATLAB workshop for female researchers coming in May 2015

By Isabell Kiral-Kornek

We are excited to announce our first post-ResBaz conference Software-Carpentry MATLAB workshop. 

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In this workshop, we are especially encouraging women to attend. MATLAB is one of the standard tools in science & engineering. It is an extremely versatile high-level programming language that allows you to do pretty much anything: from controlling hardware to recording, analysing, and visualising data. And the best thing is that you can test small parts of your program immediately. 

During the workshop, you will get a basic introduction to MATLAB’s user interface and then learn about basic programming concepts that allow you to write programs to read in and analyse your own data.We will cover how to write and use scripts, loops, functions, and conditionals.

Find a more detailed explanation, dates, and schedule here and make sure to sign up! (This workshop is limited to 30 attendees and female applicants will be given preference to.) 

 See you there!

Editing Wikipedia is good for your research [citation needed]

by Steve Bennett

As a researcher, you probably read Wikipedia articles regularly, and you might even rely on it. But have you ever thought about editing it, or writing articles from scratch? The Wikimedia Foundation, which manages Wikipedia and related projects, wants you!

What’s in it for you? You can fix the public record in an area that matters to you, address bias by covering under-represented areas or just improve your own knowledge. Or, if it’s useful to refer to certain Wikipedia articles regularly, why not improve them for your own and others’ benefit? A large number of university and school courses around the world have even incorporated it into their curricula.

Until recently, though, editing Wikipedia has been pretty tough. It required writing wikitext, an arcane markup language which starts simple (“italics”, ==headings==) and quickly becomes an unreadable mess for tables, infoboxes, and templates. However, thanks to the significant resources dedicated by the Wikimedia Foundation to this problem, the Visual Editor has finally arrived. So writing an article is now more like using a word processor.

So, to take advantage of this, ITS Research is teaming up with the University Library to run an experimental workshop. We hope to teach humanities researchers how to edit articles, while staying on the right side of Wikipedia’s rather complex set of policies. You’ll learn how to make minor corrections, start articles from scratch, use categories, infoboxes and images, in areas of interest to you. And in return, we hope to learn whether editing Wikipedia is a valuable research tool for others.

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