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Monthly Archives: March 2013

Upgrade of UNSW Virtual Microscopy Adaptive Tutorials (VMATs)

Project Description:

The project would convert the current library of VMATs using virtual slides (from the Virtual Slide repository on the UNSW server) to the new Smart Sparrow based workspace and to enable UNSW slides to be housed permanently on the AMIB.

Project Deliverables:

Upgraded VMATs and integration of UNSW virtual slides to AMIB.

User Group:

The target user group is University medical students in years 1-4. More importantly this work would enable the library of VMATs to be shared with other NBN BEST Network Partner Universities and will be readily accessible on mobile devices.

Subject Area:

The VMATs are used by the Faculty of Medicine to teach the Phase 1 and 2 Medicine program at UNSW (Phase 1 encompasses First and Second year Medical students, Phase two includes Third and Fourth year students) and Science students (approx. 1500 students per year at UNSW).

Estimated Timeline:

April 2013: Identify currently used tutorials

May 2013: Consultation with Smart Sparrow to review educational design and technical implementation to confirm what is required to upgrade tutorials. This is to ensure suggested specifications are technically feasible within the project timeline.

June 2013: Specifications finalised and signed off by all parties (including Smart Sparrow.

June – October 2013: Upgrade tutorials – this will include:

– Redoing annotations to be used in the new viewer

– Make changes to content/questions as requested

-Test changes

– An estimate for conversion and correction would be 6 hours per tutorial. This is dependent upon implementation of additional features by Smart Sparrow which may aid faster conversion of VMAT content.

October 2013 – November 2013: Begin testing VMATs in a limited number of classrooms.

December 2013: Any necessary adjustments needed to VMATs completed by Smart Sparrow.

January 2014:  Upgrade tutorials ready for use in classrooms for 2014

Finish Date:

Projected finishing date for conversion is January 2014.

Project Sponsor:

A/Prof. Gary Velan 

Key Participants and Budget:

The task of redoing annotations is dependent on functionality of Smart Sparrow workspace and could be time consuming. To reduce costs, medical students may be used to take existing annotations (on images taken from the UNSW server repository) and redone using the new technology and new images on the AMIB. Conversion would need to be checked by a discipline expert. The cost of this would be less than $20 per hour. The budget could be further reduced by sourcing volunteers to assist in conversion of tutorials.

Educational Outcomes:

– UNSW server slides will be permanently moved to the AMIB for use by the BEST Network and its partner Universities.

– VMATs available for BEST Network use

– Upgraded virtual slide viewer functionality for VMATs

– Improved user functionality: Better running performance (i.e. faster load times for slides), full integration of HTML-5 allowing use of tutorials on iPads and other non-flash home/media technology.

Future Use:

This suite of tutorials using virtual slides will provide a base for other BEST Network partners to leverage – both in adapting and using as examples.

Risk Management:

The following project risks have been identified:

Risk Mitigation strategy
Manpower/cost to redo annotations Employment of casual staff (current Medical Students) @ ~$20/hr or volunteers
SOE integration with SPR technology UNSW operating environment functions primarily on Windows XP, with Internet Explorer 8 as the default browser on many computers. Current Smart Sparrow technology operates on Firefox or Google Chrome. A short term solution to this problem would be to use computer labs that currently have Firefox preloaded into the current SOE
Management of public access Access control is desirable for VMATs on a case by case basis with BEST Network Partners. Creation of a closed network within Partners would be best to reduce exposure of content to institutions not aligned with the BEST Network
Intellectual Property Authors of VMATs need to have their authorship acknowledged, and need to retain intellectual property rights regarding who has access to try out, deploy or modify those VMATs.

 

Veterinary Anaesthesia Clinical Case Scenarios

Project Description: 

The project would develop case scenarios involving problem-solving of clinical situations commonly encountered by veterinary students during clinical practice. Veterinary Anaesthesia is a core subject of the Bachelor of Veterinary Medicine course in Australian Universities and is also a subject taught in undergraduate and post-graduate studies of Veterinary Medicine worldwide.

User Group: 

The target user group is Veterinary Medicine undergraduate students in years 3-5. The Veterinary Anaesthesia Clinical Case Scenarios will be useful for students across all the BEST Network partner universities in Veterinary Sciences courses.

Subject area: 

The Virtual Anaesthesia Clinical Case Scenarios would be used to teach units in the area of Veterinary Anaesthesiology for Veterinary Medicine students.

Estimated timeline: 

May 2013: Initiate the development of storyboards for Veterinary Anaesthesia Clinical Case Scenarios.

August 2013: Conference/meeting with Smart Sparrow staff to identify technical requirements for case scenario development. Define appropriate resources for development of clinical case scenarios and confirm feasibility of timeline with Smart Sparrow.

December 2013: Completion of the first four to six anaesthesia clinical cases. Peer review of clinical case scenarios to be performed by qualified anaesthesia specialists within James Cook University and collaborating Australian universities.

January 2013: Perform necessary adjustments to content and functionality of Clinical Case Scenarios with the aid of Veterinary Anaesthesia specialists and the Smart Sparrow team.

February 2014: Clinical case scenarios to be incorporated as a teaching and research tool with final year Veterinary students in their Anaesthesia clinical rotation.

July 2014: Presentation of Anaesthesia Clinical Cases – demonstration of use and research results at the Australian College of Veterinary Scientists Science Week conference (Gold Coast, Australia).

Project Sponsor: 

Dr. Maria Bellei, School of Veterinary and Biomedical Sciences, James Cook University. Townsville, Queensland.

Phone: (07) 47813666

Email: maria.bellei@jcu.edu.au

Key Participants: 

Maria Bellei; JCU, School of Veterinary and Biomedical Sciences

Chris Christensen; JCU, School of Medicine

Jo Rainger; University of Queensland, School of Veterinary Science

Project Outcomes: 

The Anaesthesia Clinical Case Scenarios will provide the following outcomes:

–          Allow students in their final year of Veterinary Medicine to engage in critical thinking and interactive learning during their Anaesthesia clinical rotation;

–          Complement the student’s knowledge of cases they may not have been exposed to during their Anaesthesia clinical rotation (10 days duration only per group);

–          With the aid of the web analytics of Smart Sparrow, the Clinical Cases will help educators identify critical areas where misconceptions or knowledge gaps are common in the subject of Veterinary Anaesthesiology, or areas where students have difficulties in learning;

–          Contribute to the students’ clinical experience and knowledge without the use of live animals, staff and medical resources, reducing the total cost of Veterinary Education for the University;

–          The Anaesthesia Clinical Case Scenario can be adapted to perform as a clinical assessment tool that evaluates individual student performance at the end of their 10-day clinical rotation.

Future Use: 

Veterinary Anaesthesia is a large component of the daily routine of a Veterinarian in clinical practice.

The Anaesthesia Clinical Case Scenarios can be used primarily for teaching and assessment of final year veterinary students.

Simplified scenarios involving basic knowledge of anaesthesia can be useful for teaching of students in less advanced years of the Veterinary Medicine course (Years 3 and 4) whereas the inclusion of more advanced clinical reasoning and knowledge of anaesthesiology is suitable for final year students.

The Anaesthesia Clinical Case Scenarios can be adapted and applied to teaching of students enrolled in Veterinary Nursing courses throughout Australia as well.

Risk Management: 

The project team has identified three key project risks:

  1. The project team, with the aid of Smart Sparrow, may not be able to complete the Anaesthesia Clinical Case Scenarios in time for testing and full review prior to their use in February 2014. This risk is highly likely to occur but is low priority as should the Anaesthesia Clinical Case Scenarios not be completed by February 2014, the project can run the Anaesthesia Clinical Case Scenarios from July 2014 onwards during the final year students’ fortnightly clinical rotations of semester 2.
  2. Smart Sparrow may be unable to develop the right technology. This risk is unlikely to happen but would significantly compromise the content of the Anaesthesia Clinical Case Scenarios. In such case, the project would have to be redesigned to meet the needs of Veterinary Anaesthesia students.
  3. The Sponsor and project participants are unable to commit time and resources to successfully complete the project. If this is the case, the project team shall apply for an extension of the project deadlines, pending that the need for such extension can be justified, or seek suitable replacements to complete the project.

Virtual Cytology and Adaptive Tutorials for postgraduate specialist education in pathology

Project Description:
  1. Development and delivery in digital form, including to rural and remote sites, of scarce educational materials in cytopathology (virtual cytopathology slides and associated VMATs).
  2. A project using the described material to evaluate whether this digital educational strategy can be successfully employed to teach cytopathology to anatomical pathology trainees in the same way that virtual histopathology and associated VMATs have been used to teach UNSW undergraduates.
User Group:
  •  Anatomical Pathology trainees Australia-wide.
  • At the completion of the project the material will be useful  and available to all pathology trainees (post-graduate doctors specialising in pathology), and all Pathology specialists Australia-wide via the Royal College of Pathologists of Australasia.

At completion of the project both the results and material will be relevant to other user groups such as cytopathology scientists, pathology specialists and medical students Australia wide.

Subject area:
  • Virtual cytopathology and associated adaptive tutorials for postgraduate specialist education in pathology
  • Anatomical Pathology/Cytopathology
Estimated timeline:

The project is designed to run in 2013 and 2014, as follows:

The project involves:

Resources and lead time

  1. Ethics approval has already been obtained from HREC at UNSW for the project and approval has been obtained from the Royal College of Pathologists of Australasia for this project and to involve its AP trainees. There will therefore be no delay in initiating the work.
  2. Assessing and Collecting relevant and appropriate traditional glass cytopathology slides from an Anatomical Pathology Department for development of electronic educational material – this has been be facilitated by the assistance of Assoc/ Prof Elizabeth Salisbury and her senior cytology scientist. This part of the project is completed.
  3. Scanning/image acquisition of the virtual slides by HMU (UNSW) has been completed.
  4. Securing server space to store and distribute the virtual slides

Estimated Future Timeline

  1. Developing adaptive tutorials to wrap around the virtual cytopathology slides (6 months)
  2. Delivering a “pilot set of adaptive tutorials (around cytopathology slides) to be made available via the RCPA education portal for user evaluation and assessment. (3 months)
  3. Recruiting participants for the trial (trainees from RCPA)(3 months)
  4. Subsequent 3-month trial (early 2014) will evaluate the effectiveness of this educational package for Anatomical Pathology trainees (postgraduate doctors specialising in pathology) with a particular focus on its suitability for use at rural and remote sites. (3 months)
  5. All educational materials developed for this trial will be made available to all trainees nationwide via the RCPA education portal immediately upon completion of the trial. (1 month)
  6. The project team will analyse the acceptance and effectiveness of online virtual cytopathology as an instructional tool in anatomical pathology, including for rural and remote trainees. (3 months)
  7. Publication of results is anticipated at the completion of this project.

The desired date for all education material (vslides and VMATs) to be set up on website for trial is Jan 2014. End date mid 2014. Analysis of results end 2014.Publication early 2015.

Key Participants and budget:

Project managed by UNSW (Dr Simone Van Es, A/Professor Gary Velan and Professor Rakesh Kumar)
In collaboration with RCPA (Dr Wendy Pryor) and the Department of Anatomical Pathology at POWH (A/Professor Elizabeth Salisbury).

  1.  Development of website to act as an interface for housing links to VMATS and virtual slides for each arm of the trial – MCSU – Jake Surman – approximately 40 hours.
  2. Support and trouble-shooting assistance with the VMAT development from the BEST project officers:  21 VMAT cases to develop in addition to 9 VMAT cases to develop for an small post trial “exam”. Estimate at 5 hours per case so approximately 600 hours of their time.
  3. Assistance with analysis and statistics – estimate 60 hour
  4. Assistance with purchasing and developing heat map visual overlays for analysing the  drag and drop questions in the VMATS – 600 hours.
  5. Organisational assistance from BEST project officers with recruiting participants via RCPA – 60 hours

Note: The costs under the resources and lead time has already been absorbed by the project group.

Educational Outcomes:
  • The approach to implementation and evaluation during both the pilot and trial phases of the project will promote networking for trainees across Australia.
  • The educational materials distributed via the RCPA education portal after the trial could be used by remote trainees for networked online study groups.
  • Delivery of these educational materials and evaluation of the educational benefits will be nationwide for the “pilot” and trial phases of this project. Subsequently, the virtual cytology slides and the associated online tutorials will be distributed via RCPA to all Anatomical Pathology trainees nationally.

Sustainability beyond 2013

  • Because ongoing access to educational materials will be via the RCPA education portal, the benefits of the project will continue well into the future.

Targeting to multiple disciplines

Although this project will examine the educational effectiveness and efficiency of virtual cytopathology, the results will translate to virtual histopathology and haematology as well. In addition, the educational material developed by this project could in the future be made available to cytopathology scientists and trainee cyto-scientists.

Project Sponsor:

The project will be led by Dr Simone Van Es (anatomical pathologist and lecturer in Pathology at UNSW) who is enrolled for a PhD in the Department of Pathology at UNSW, supervised by Assoc Prof Gary Velan (Head of Department) and co-supervised by Professor Rakesh Kumar (UNSW), Dr Wendy Pryor (Director of Education, RCPA) and Assoc Prof Elizabeth Salisbury (Director, Department of Anatomical Pathology, POWH).

Risk Management:
Risk Mitigation Strategy
Intellectual Property
  This project is partly funded by the    SPECIALIST TRAINING PROGRAM – RURAL SUPPORT INITATIVES 2012-2013 (RCPA/ DoHA) so any Intellectual Property rights and title to, or in relation to, the Project Material will be vested in RCPA. We may sub-licence its rights subject to obtaining RCPA’s prior consent to the sub-licence, such consent not to be unreasonably withheld or delayed.RCPA also grants a royalty-free and licence fee-free, worldwide, non-exclusive, licence to use the Intellectual Property in any research papers created in the course of undertaking the Project
Time delays
  Due to complexity of proposal and number of steps dependent on separate independent bodies, there is the possibility of time delay in roll out of the project Unlikely as Project sponsors and Project managers have already secured significant resources, structure and lead time for this project
Technical issues
  Technical difficulties in development of user-friendly VMATS that are based around virtual cytopathology slides of large file size Unlikely but proof of principle to be obtained on initial pilot of 3 virtual cytopathology slides and associated VMATS on RCPA education portal

Bringing macroscopic images of disease to AMIB

Project Description

Make a well curated collection of ~1500 macroscopic images of disease and related metadata available for use in AMIB by BEST Network partners

User Group:

Undergraduate medical, nursing and allied health students. Postgraduate radiology and pathology trainees (medicine).

Subject area:

Anatomical Pathology – macroscopic appearances of disease

Estimated timeline:

1. Redigitise and store ~1500 images from IOD collection in uncropped but larger format – 6000 x 4000 pixels (see xxx to view cropped 800 x 600  images of same). Time – one month. Size 10MB x 2000 = 20TB.

2. Extract relevant data from IOD database, edit and add other metadata to all images. Time: 60 hours

3. Recode disease and organ terminology to SNOMED standard. 400 hours.

Key Participants and budget:

Nick Hawkins: originator of IOD database (in kind)

BEST Network Image Data manager: $40 per hour x 500 hours =$20,000 (?in kind contribution by BEST)

External 35mm transparency digitizing service: $2000

Educational Outcomes:

Creation of relevant image resource for future BEST network projects.

Provision of substantive metadata collection, including disease, organ, path processes, clinical history, macroscopic description.

Images amenable to annotation, but not part of this project

Images relevant to multiple undergraduate curricula

Project Sponsor:

Nick Hawkins

Risk Management:
Risk Mitigation strategy
Image quality:
  Original 35 mm slides of poor quality because of suboptimal storage (Unlikely but to be reviewed)
  Digitisation process results in inferior image, or need for photo-manipulation too time consuming. Unlikely but proof of principle to be obtained on initial pilot of 50 slides.
  Uncropped images not usable in AMIB viewer for technical or aesthetic reasons. Unlikely but proof of principle to be obtained on initial pilot of 50 slides
Image metadata
  SPR unable to implement suitable labeling system for disease and organ.  
Image display
  SPR unable to implement suitable scaling process to allow display/zooming of higher resolution images Unlikely but proof of principle to be obtained on initial pilot of 50 slides.
Intellectual property
  IP not transferable Images the property of UNSW an d original specimens the property of UNSW
  Owners unwilling to assign images to BEST network or allow use of image by network partners As above. Use of individual image in BEST Network (and hence free use by others for educational use in Australia) is explicitly agreed to by owners of copyright (UNSW).
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