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May 2016

An invitation to the world of digital archives

A few weeks ago a select group of Arts researchers got together to explore and investigate the mysterious world of digital archives. Archives are extremely important for HASS researchers, or anyone interested in investigating culture. Historical, literary, artistic, and personal - there are so many different kinds of stories that can be told through the neat organisation of an archive. Explorations through texts, images, or objects often turn into something of a detective story, with the researcher piecing together clues found on dusty shelves.

(Above image: not a very well organised archive)

Over the past decade or so the dust is slowly being shaken off, and archives are being digitized, made searchable and shareable. This is a great opportunity for researchers working with digital objects of any kind, be they photographs, video, important historical documents, or recordings of interviews. Now you can organise your digital items into an archive, one that you can access anywhere and that is easily searchable. Gone are the days of scrolling through hundreds of pictures and PDFs until you find what you want! One tool that is great for creating and exhibiting digital archives is Omeka.  

In our workshop we took a brief look at some sites that are currently using Omeka. We listed some pros and cons of these public facing sites, and explored the collections and exhibitions of each particular site. If you would like to have a glance at some examples of what Omeka can do, have a look at the showcase here: https://omeka.org/showcase/

Among others, we analysed the beautiful Peacock Room: http://peacockroom.wayne.edu/

And the gothic, historical archive of medieval Irish architecture http://gothicpast.com/  

These two very different Omeka sites provided us with an idea of the different ways that Omeka can be used to showcase items in an archive. We also discussed some difficulties of the site. These were usually issues of navigation within the collections - as a group, we discussed the importance of clearly setting out all the items in an archive in a way that makes sense to researchers. It is the story around digital objects that makes them interesting and accessible - which brings me to metadata.

In the final section of the workshop we discussed the importance of organising your archive, and the way that metadata is used to position items within that digital space. Attendees learnt how to sign up to an Omeka account, and how to add items to their archives:

Having explored some other Omeka sites, we knew the importance of navigation and organisation within an archive, so we spent a bit of time thinking about how to plan the various collections or exhibitions that researchers might want to construct.

After the workshop several researchers created their own omeka sites, and have been hard at work filling them with intriguing digital objects. I am so excited to see how these projects grow into important collections. Hopefully these digital spaces will help researchers tell the stories that have inspired their work.

Of course, there is much more to learn about creating and maintaining digital archives. In the next workshop we will look at the some useful, technical tools in Omeka. By the end of the workshop attendees will revise how to add items, and write a master metadata plan into an Omeka site. Attendees will learn how to change the navigation and appearance of a site (useful for public-facing archives). We will also learn how to upload a .csv file of objects into Omeka, how to write descriptive pages of text into an archive, and how to construct exhibitions and collections.

As well as gaining the technical skills to build a digital archive, researchers will be given the time to discuss their specific projects with a group of supportive researchers and archivists. This workshop is for anyone interested in digital archives, so no matter whether you are just at the beginning of your project, or if you’re well into building your collection, all are welcome.

It will be on Thursday 2nd June, from 4:30pm - 6:30pm in the CoLab. For more information, and to register for the event, please follow this link https://www.eventbrite.com.au/e/omeka-training-digital-archives-and-exhibitions-tickets-24669545274

I’m really looking forward to seeing you all there!

Meredith 

May 30, 2016
Looking Through 3D printed binoculars

A post by Emilie Walsh


Hello Everyone! I’m Emilie, your new Research Community Coordinator for CAD and 3D printing at Research Bazaar.

I am a PhD candidate in Fine Arts at the Victorian College of the Arts, and my journey to 3D printing started out by genuine curiosity: I was first intrigued by the MakerBot 3D printer we have on Campus at the VCA, and wondered how it could be of some use for me.

While most artists have an interest in 3D printing for its amazing sculptural potential, I was first driven to use it in a more functional way.

My practice is image based, and I work in video, photos, drawing and printmaking, rather than with sculpture or spatial practice. However, I am always looking into new ways of displaying and showing images, and I have a strong interest in viewing devices such as vintage View Masters.

A vintage View Master

I love the intimate relationship those devices create between the image and the viewer. To look through an object and discover a hidden image only you can see, reminds me of strong childhood memories like looking through a kaleidoscope, binoculars or other camera toys!

Originally posted by rhetthammersmithhorror

I wanted to be able to display my work through a viewing device, and this is when I started investigating 3D printing, as a way to get what was in my mind into reality.

Come and have a peep tonight @GPatonGallery ! closing event tonight 5-7pm! pic.twitter.com/jecLSo2wvs

— Emilie Walsh (@emilouwalsh)

23 March 2016
I first came into contact with Research Platforms via a research tool speed dating event run at the VCA. I was introduced to Vincent Khau, and he was responsible for most of my training!

I attended a few workshops for CAD software (TinkerCAD, Autodesk Fusion 360, Autodesk Inventor) with Research Platform to learn how to design my viewing device. I wanted to design something that looked like a pair of binoculars, but with the ability to insert photo slides into it.

CAD in full swing!!!! #inventor #resbaz #cadventure pic.twitter.com/eRDHJm8txT

— Aliza w (@awajih08)

1 February 2016
I was quickly amazed by all the possibilities, as well as how easy it was, even if I had no engineering or industrial design background! TinkerCAD is the easiest thing and it is so playful! I believe it is the best software to be introduced to CAD 3D modelling: in addition to how easy it is to use, it’s free and you don’t even need to download it to your computer as it is a web-based application.

I was able to design my first 3D model to print, achieving in plastic what I had pictured in my imagination! How magic!

 3D printed binoculars before being painted and assembled.

Come and check those 3D printed binoculars at the @GPatonGallery ! #resbaz #3Dprints pic.twitter.com/nBCHFtriBe

— Emilie Walsh (@emilouwalsh)

22 March 2016
The nature of the plastic, almost toy-like in quality, really did suit what I was using it for. My slide-viewer binoculars have a fun and easy-to-handle nature, which allows visitors in the gallery to feel confident using them. I’ve sanded it to get a smoother finish, covered with multiple layer of spray putty (a filler to reduce the facets), and multiple layer of glossy red paint to make it attractive and fun to play with!

In the future, I would like to keep working with 3D modelling to create some more complex viewing devices, maybe an articulated one for the viewer to activate it and really interact with the images. While usually working with a 2D medium, 3D printing has literally given a new dimension to my art work, opening new perspectives on the way we look at images.

If you feel like 3D modelling and 3D printing is something you would like to learn about, I’m going to be running workshop with Research Bazaar. Be touch with me or one of my amazing colleges of the CADventurer team at Research Bazaar.

find me on twitter: @emilouwalsh

emilouwalsh@gmail.com

May 28, 2016 1 note
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.

@JasamineCB taking the lead for our #3Dslicer training at VIFM. Everyone seems quite impressed! @resplat #resbaz pic.twitter.com/jAjjrtevjP

— Louise van der Werff (@LouWerff)

May 16, 2016

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.

@LouWerff impressing the staff at VIFM with #3Dslicer potential right now. #3Dprinting Ping @ResPlat @PJMignone pic.twitter.com/pjMEPhCCfB

— Deluxe Minimalist (@Hincerooney)

April 19, 2016

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.
May 26, 2016 1 note
#VIFM #3DSlicer #anatomy #3dmed #Louise #jasamine #jas #resplat #3dmodelling #medical #image #procesing #resbaz #MDHS #unimelb #forensics
The loneliness taboo: Why doing a PhD doesn’t have to be an isolating experience

By Nikki Rubinstein and Christina Tuke Flanders

As a current PhD candidate, I know that doing a research degree can be an incredibly lonely undertaking. When things get tough, it’s up to you - and only you - to pull yourself through and grasp for the next hopeful idea. You often find yourself re-doing the same things over and over again. My supervisor likes to say that’s why it’s called RE-search. But that feeling of banging your head against a wall can be an extremely demoralising and isolating experience. Especially if you have no one to share it with.

https://www.youtube.com/watch?v=5RSMzUsZolI

We often hear about illnesses like heart disease, cancer, stroke - but what about loneliness? Is being lonely just something you need to ‘pull yourself out of’ or does it have more far-reaching effects? Should loneliness join the physical ailments in our discussions on health?

A recent study conducted at Brigham Young University suggests that the answer is yes; loneliness is detrimental to our health. In fact, results revealed that on average loneliness increases mortality rates by between 26-30%! Worryingly, they noted that social factors were a greater predictor for mortality in non-elderly populations. I’m concerned since I would definitely count myself among the non-elderly category.

via GIPHY

As a critical thinker, you may be saying: “this is only a single study, the results can’t be that impressive”. So let me tell you, this research study comprised a meta-analysis of 70 journal articles, totaling almost 3.5 million study participants! It is the largest study of its kind and not to be ignored.

If I haven’t yet convinced you that loneliness is a major health concern, let me add that loneliness can have detrimental effects on sleep, self esteem, cortisol levels and general cognitive functioning, as well as acting as a risk factor for other potentially-debilitating mental health issues such as depression and anxiety. So now that we’re on the same page about loneliness being a health concern, what can we do about it? Well, I’m so glad that you asked!

ResBaz conference attendees connecting and making friends

The best way to combat loneliness is with social contact. But beware: not all social contact is equally beneficial. Have you ever been in a room full of people and felt utterly alone? If you have, you’ll know what I mean about social contact not being enough on its own to stave off loneliness.

Rather than heading to Flinders Street at peak hour, humans need social contact that provides real value. What do I mean by value? Something very different to the bargain bin at K-Mart. I mean anything that creates a sense of belonging, or a sense of community. While I’m in the process of defining terms, I’d like to introduce you to the concept of social capital. This term describes the relationship networks that allow a society to function effectively. Social capital includes networks such as volunteering associations, friendship networks, religious communities and hobby club activities.

Wake up to Yoga! at the ResBaz 2015 conference

Our best defense against loneliness is through rich social capital. Within the university environment, this can be found through clubs, departmental friendships and - the more recent addition - the Research Bazaar (or ResBaz). ResBaz is the community building arm of Research Platforms (a service department within Infrastructure University services). The beauty of ResBaz is that it is run by researchers for researchers.

Having an intimate knowledge of the trials of doing a research degree, ResBaz Research Community Coordinators seek to offer researchers a haven where they can meet like-minded people and find support for difficult-to-master digital tools. Some ResBaz activities include (but are not limited to): training workshops, digital tool speed dating, games nights and lunchtime craft sessions. Did I mention that these are all free?

Research Community Coordinators with attendees at the ResBaz 2016 conference

Psychologist, Dr Christina Tuke Flanders, has recently come on board at ResBaz as a Training Consultant. I asked her what are the other benefits of being part of a community like ResBaz? She has observed that: "a community like ResBaz facilitates feelings of connectedness by building relationships with peers and enhancing a sense of belonging.”

She added, “In Psychology we talk about protective factors that promote positive mental health. Firstly, building relationships like students do at ResBaz can act as a buffer from feelings of alienation and anxiety. Secondly, having a place that students can visit like the CoLab space in Old Quad engenders a sense of belonging. Belonging gives a person a sense of purpose, meaning, and social control; all which are contributors to positive mental health.” Dr Tuke Flanders reflected: “I recall that my doctoral research was a rather lonely existence. I would have loved to have access to a place like the CoLab to access mentors who could help me with the digital tools for my research. I hope more students take advantage of this service.”

My interview with Christina

ResBaz is an all-inclusive community, focussed on enriching the social capital of the university for researchers. ResBaz is located in the CoLab working space, Room G07, The Old Quadrangle. Come by for a drink and a chat, and let’s do our bit to reduce the degree of isolation within the university environment.

ResBaz 2015 conference attendees in the Old Quad

May 20, 2016 1 note
#community #nikkirubinstein #ctf #mentalhealth #loneliness
FREE Basics to RStudio training session: May 31 and June 1

Have you met my friend R? R is the kind of friend of who will tell you when you’re doing something silly. R is the supportive type. Whatever you want to do, R will oblige. R is very literal, following instructions to the letter. So you have to be careful what you ask of R. But with only a few instructions, R is willing to do the majority of the grunt work. I am thankful for the day that the programming language R entered my life.

http://www.freestockphotos.biz/stockphoto/1720

R is an open source functional programming language with a large online community of researchers. We ran a Beginner’s to R/RStudio Workshop on the May 31st and June 1st, where we introduced an eager group of researchers to the benefits of using R.

The workshop began with each table of attendees coming up with a table name (much like you would create a variable name in R!). The five tables were: The PiRates, WeR7, The Roos, Rmageddon and PooR Decisions.

Benefit no. 1026 of R at the @ResPlat RStudio workshop: cool team names @nikkirubinstein #datascience @rstudio pic.twitter.com/AS69kuWpLy

— Tim Esler (@TimEsler)

May 31, 2016

The first day of the workshop was spent introducing researchers to basic programming concepts, such as variables, different data types, subsetting data and inbuilt functions. The afternoon heated up as we moved on to learn about how to create our own functions and then to create publication quality graphics using the ggplot2 package.

Learning about different data types with @TimEsler #R @ResPlat #DataScience pic.twitter.com/ch1ddHQMOZ

— Nikki Rubinstein (@nikkirubinstein)

May 31, 2016

Day 2 commenced with a discussion on control flow that revealed that on Thursdays Rmageddon are feeling non-cooperative and on Saturdays PooR Decisions can be found seeking mates. Vectorisation was shown to be a faster way of applying a function to a set of data and researchers quickly picked up the coding benefits. The afternoon was rounded off with a session on data manipulation using dplyr.

.@TimEsler finishing up the workshop with dplyr #R @ResPlat #DataScience @TimEsler pic.twitter.com/RU07BLHNno

— Nikki Rubinstein (@nikkirubinstein)

June 1, 2016

This would not have been possible without the wonderful helpers, who volunteered their time, enthusiasm for coding and wisdom to provide support to our workshop attendees. Thank you Tiane, Tom, Yamni and Tim!

We just completed our two-day workshop on R for beginners! Well done to all of these new #DataWranglers 👏👏👏 pic.twitter.com/6xdPfrDls2

— Research Platforms (@ResPlat)

June 1, 2016

For the full twitter story see our storify post.

May 19, 2016 1 note
#NikkiRubinstein #R #RStudio #DataScience #Trainings
SOAP Discussions: Engineering

By Vincent Khau

Recently, I was kindly asked to do a presentation for SOAP (State of the Art Platform) by Sophie Neate, Nina Gilbert and her colleagues centering around 3D scanning, 3D printing, with a focus on engineering and the distortions that occur in the process of transforming a real-life model into a digitised file. This talk formed a part of their three series interdisciplinary discussions of topics from economics, meta-data, and identity, to text, Japanese screen culture, and engineering at the KINGS Gallery on Kings Street.

That’s me presenting! Not your normal lecture space!

It was a really exciting opportunity to be able to talk about a core technology to my work and share with an audience of artists and the general public the wonders of 3D printing and scanning technology.

We started the discussion off with exploring the wide breadth of methods to obtain a 3D digital model. These methods varied from using existing online repositories like Thingiverse, Shapeways, and even the Smithsonian Museum where communities share their models and scanned data for everyone to use! Further to this, we talked about learning 3D modelling from scratch using a variety of online tutorials (or coming to one of my or Aliza’s ResPlat workshops) would allow artists to further edit these models are even build their ideas from scratch! Another exciting approach is to use 3D scanning and on the day I brought along an Artec Eva and did a small scan of Sophie to illustrate how physical information can be distorted through the scanning process. An example of this can be clearly seen in the following images where the Engineering Workshop scanned a 4000 year old Mesopotamian chariot.

Before…

After! Fully scanned digital model.

So what does one do when one has a 3D model? Well, why don’t we 3D print it! I had brought along an Up 3D printer and showed how designs can be quickly prototyped in a variety of different materials from plastics, to resins, and even metals using a range of different 3D printing techniques. 

As a part of our discussion focus, we finished the presentation on how I had applied 3D printing to my engineering research in developing active adaptive landing gears. I displayed our group’s prototype on a rotating platform and showed that even though the parts had been 3D printed, they still had structural integrity to live up to basic engineering expectations. Further to this, by 3D printing all the parts, we were able to rapidly prototype various designs and accelerate the design process. The audience all loved the little prototype and came up to it after the presentation to engage with the model.

I’d like to thank Sophie, Nina and her colleagues for giving me the opportunity to present as part of their initiative and hopefully it has inspired the audience to engage with this technology!

May 19, 2016 2 notes
#SOAP collective #3dprinting #3dmodelling #kingsgallery #engineering #resplat #3dscanning
Blog awards: May (12/05/16)

We can’t believe it’s May either. Here are the top three posts from the last month:

1. “Seeing things differently” by Pip Karoly
Data Wrangler & MATLAB champion Pip takes the gold this May with her post on the benefits of data visualisation, and the tool D3. Pip presents examples of her own work: “My research is in understanding brain waves - especially when things go dangerously wrong, like they do during a seizure.”

2. “A Seminar to remember!” by Warda Syeda
Also a Data Wrangler, Warda is one of our newest team members and is writing up a new MATLAB extension curriculum. Here she recaps a seminar hosted by the Melbourne Brain Centre looking at atlases of mouse and human brains! 

3. “3D Printing at Austin Health” by Jasamine Coles-Black
Jas first wrote this piece as a guest-blogger, looking at how 3D Models & can help educate trainee surgeons at the University of Melbourne. Nowadays, Jas is one of our newest Research Community Coordinators as a CADventurer! 

May 12, 2016
#blog awards #awards #pip #pippa #warda syeda #warda #jas #jasamine coles-black #pip karoly #blogawards #best of #may
Medical image processing @ Research Platforms

Post by: Jasamine Coles-Black

Hello everyone! I’m Jas, your new Research Community Coordinator for 3D Slicer at Research Platforms.

I first came into contact with Research Platforms via 3D Med, a joint collaboration in medical 3D printing with Austin Health, founded by ResPlat legend Paul Mignone and vascular surgeon Jason Chuen. This initiative included the “3D Printing for Medical Applications Seminar”, and led me to enrol in Louise van der Werff’s 3D Slicer Alpha workshop last year. For those of you who don’t know, 3D Slicer is a software package for image analysis and scientific visualisation. The best part? It’s free!

A kidney tumour model segmented from a patient’s CT scan at Austin Health using 3D Slicer, to aid presurgical planning. Watch this space for the 3D printed end result!

Just a little bit about my background. I’m an aspiring surgeon in my final year at Melbourne Medical School. It was this interest in surgery that led to me to discover the medical applications of 3D printing, which are varied and far ranging, and all equally amazing.

Some pretty inspiring examples in the literature would include bioengineering and tissue engineering, interventional planning, medical and surgical training, anatomy teaching, customised prostheses and implantable components, patient education, and forensic medicine.

As someone with who struggles with Microsoft Word, and had no previous medical image processing experience, this for me was truly diving off the deep end. For someone of my background, the promised land was truly far, far away. And like many clinicians, I was initially unsure about how much benefit medical image processing could truly bring to my research.

This leads me to my point - while there seems to be a huge amount of enthusiasm for the applications of 3D printing in the wider medical community, a significant barrier remains. Despite their enthusiasm, clinicians often lack the technical skills required to segment medical images and 3D print models of their patient’s anatomy.

A generalised 3D printing workflow for medical models.

The generalised 3D printing workflow conundrum facing clinicians.

Following this initial experience, I continued to collaborate with Research Platforms as a Helper for 3D Slicer. It was during this time that I truly began to appreciate what Research Platforms was all about – namely, free training to help you do your research better, with as few barriers as possible.

This too, has been my goal with the 3D Med initiative based at Austin Health – information and technical know-how about medical image processing and 3D printing should be made available to as many clinicians as possible who are interested in applying this technology to their research.

@ozvascdoc presenting at #RACS16 about aortic #3Dprinting workflows we’ve developed @Austin_Health #3Dmed pic.twitter.com/Yo5zjudrVx

— Jasamine Coles-Black (@JasamineCB)

May 3, 2016

Surgeons as a whole have a pervasive reputation for being luddites. While this can sometimes be true, the 2016 Royal Australasian College of Surgeons Annual Scientific Congress in Brisbane set out to change this perception, with the theme “Surgery, Technology and Communication”.

I’ve just returned to Melbourne, fresh faced and inspired by the work of the myriad of amazing local and international speakers invited to present at the congress. Themes that were raised during this conference included big data and data management, novel methods of teaching trainee surgeons, virtual and augmented reality, and 3D printing (if you haven’t figured it out by now, it’s kind of my personal interest).

Other fascinating topics that were raised included the use of robotics and simulation in surgery, with processed medical images being used as the inputs for the surgical robots to do their thing.

Fascinaing talk on the marriage of medical image processing and #robotics in surgery #3Dmed #RACS16 pic.twitter.com/2A52MLfHqE

— Jasamine Coles-Black (@JasamineCB)

May 3, 2016

Hang on…

Is it just me, or does it seem as though more surgeons ought to be visiting us here at Research Platforms? :D

Soooooooooooooooooooo… What can you do for me, Jas?

Well, I’m glad you asked! As one of the Research Community Coordinators for 3D Slicer, I’ve been tasked with upskilling the medical research community in medical image processing, 3D modelling, and 3D printing. At Research Platforms we’re also all about collaboration and network building. In essence, I’d also like to put you in touch with other individuals with similar interests, but complementary skill sets, so you can scratch each other’s backs like happy lab monkeys.

Scratch that collaborative research itch!

And to all 3D Slicer course alumni: how have you been using 3D Slicer in your research? Having attended the introductory 3D Slicer for Beginners course, have you got any suggestions for intermediate/advanced extension courses that’ll help you do your research better? We’d love to hear from you!

I can be reached at: jasaminecb@gmail.com or send a tweet my way @jasaminecb - I look forward to hearing from you!

May 9, 2016
#3dslicer #3dprinting #anatomy #resplat #resbaz #austinhealth #CAD #3Dmodelling #DICOM
ResBaz: tinkerCAD and Fusion 360

by Vincent Khau

Three years on and the Research Bazaar conference is still running strong and pumping out new training curricula in 3D modelling to teach researchers from all skills and backgrounds. And it’s a skill that is highly sought after with full two full classrooms of PhD students and researchers attending both the tinkerCAD and Fusion 360 sessions.

For those who had no experience in computer aided design but still wanted to engage with innovative technology like 3D printing (um who doesn’t?) we started off with tinkerCAD - an easy to use web-based 3D program. But don’t let it’s playful interface and simplicity fool you, it’s a software that’s more than capable of producing designs to create custom laboratory equipment, early prototypes as well as editing existing CAD models.

PhDa and researchers experimenting with #tinkerCAD at #resbaz pic.twitter.com/eVDlCiUi9g

— Vincent Khau (@thevinniek)

February 2, 2016

For those looking to learn more about advanced CAD packages and looking to gain the skills to create more complex parts, we got stuck into a completely new offering called Fusion 360 where we explored free form modelling. In the 1.5 hours available, we covered a fast paced workshop where the attendees were introduced to the interface of Fusion 360 and its navigation tools, and then went on to learn how to generate custom bone prosthetics using a model from real data developed by our 3D Slicer expert Louise!

@thevinniek is so popular!! Learning new CAD software Fusion 360! #ResBaz @ResPlat pic.twitter.com/h5uFvB1yxs

— Aliza w (@awajih08)

February 3, 2016

To contextualise why we had been learning all of this CAD, as well as to inspire students to continue and pursue it further, the great Paul Mignone demonstrated how to transform the newly formed models into a physical object using 3D printing over at the Engineering Workshop. By producing tangible visual products, conveying difficult aspects of research can be easily broken down for others to understand.

How do you 3D print? @PJMignone explains the mysteries away at #resbaz pic.twitter.com/3ymAENeOc6

— Vincent Khau (@thevinniek)

February 3, 2016

All this could not have been achieved without my awesome team of helpers (left to right: Bobby) who floated around during the workshops to answer any questions. Shout out to Paul, Louise, Aliza for all the encouragement and the support.

My #ResBaz team for #tinkerCAD and #fusion360! pic.twitter.com/tl5EGWZXtY

— Vincent Khau (@thevinniek)

May 3, 2016

If you’re interested in learning about CAD, there are many ways to contact me

Hacky Hour (every Thursday 3-4pm Tsubu Bar)

PhTea (every Tuesday 10-12pm at the CoLab, Old Quad)

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Cheerio!

May 3, 2016
Do you wish that your data acquisition can be done easier? Here’s how I do it

by Marcella Purnama

Hi everyone! My name’s Marcella and I had been the videographer of Research Platforms for a year and a half — a role I stepped down from earlier this year. The reason? I wanted to focus on my thesis. And here’s my story.

I’m currently finishing my Master of Publishing and Communications at the University of Melbourne, and even though it’s a coursework program, working at ResPlat inspired me to do the minor thesis stream. I’ve just sent the 13,199-word paper to my supervisor for final approval, and I would be submitting it this Friday.

So yes, I’m a legit researcher now. (I wish.)

My thesis focuses on the audience emotional engagement and how this affects the success of a Young Adult book. In this thesis, I’m trying to figure out whether publishers and authors’ attempts in engaging readers through social media are effective, and how the emotions expressed by readers on Goodreads reviews relate with the success of the books. I draw my case study from John Green’s four YA books.

(Ps. If you’d like to know more about my thesis, I’ve written an article on it for The Conversation.)

But first of all, the data…

In determining the ‘audience emotional engagement’, I decided to use the Goodreads reviews of John Green’s four books. These were the things I needed: the reviews, the users’ names and the users’ ratings of the books.

My supervisor had no experience in scraping data from Goodreads, but a colleague of his had used the software OutWit Hub Pro to scrape the reviews. This colleague showed me how to use the program, and I played around with it for a few hours before calling it quit.

Using OutWit Hub Pro, I decided, was a pain.

Here’s how my data from OutWit Hub Pro looks like:

The data that I had gotten was not clean at all, and it required many trials and errors in trying to get only several reviews. Plus, I had doubled up the data, for the program scraped both the short and long versions of the reviews. I had headaches then, but I remembered one thing: I worked at a research department.

I came to Yuandra, one of the ResCom coordinators, and asked whether he had a better solution to my problem.

…And he did!

He taught me to use the programming language R to scrape the data.

It took him one coffee meeting to teach me how to run the program. My supervisor estimated that it would take at least a month to get all the data that I needed. I had mine ready in a matter of hours.

Needless to say, he saved my thesis, allowed me to go on a two-month holiday (true story) and gave me the luxury of time. Here’s what my data from R looks like.

There’s an easier way to get your data, only if you know who to ask. I’m certainly lucky to know who.

So if you’re grappling with data acquisition, I highly recommend going to our upcoming Data Acquisition Training that is being held on 12-13 May 2016.

There, you can ask questions and talk about the most effective way to get your data. There are talks on survey tools, mobile data collection, scraping and more!

It’s a free training, but do you need to apply for it. Simply go to https://www.eventbrite.com.au/e/introduction-to-data-acquisition-beginners-tickets-24973908633 and you’ll find all the information you need.

Oh, if you’d like more information about Research Bazaar and the trainings we offer, go to melbourne.resbaz.edu.au or tweet us @ResPlat!

May 3, 2016
#Marcella #data acquisition
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