1. Medical Image Analyzer - Final report
Benjamin Aribisala – Lagos State University - Nigeria
e-Research Summer Hackfest – Catania (Italy)

2. Outline Scientific Problem Aims and Objectives
Works done during the Hackfest
Results
Future plans
Summary and Conclusions
Appreciations

3. Scientific Problem
Some of the challenges in the field of medical image analysis
Data is money – Equipment and samples are expensive
Shortage of image analysts
Limited collaboration
Science Gateway can help in solving medical image analysis problems by making e-infrastructure available for
Image repository
E-service – image analysis
Collaboration
There is no medical image analysis e-infrastructure in Africa

4. Aims and Benefits AIMS To develop a repository for medical images
To develop a platform that will allow users to be able to upload and process their images.
BENEFITS
It is our hope that the proposed platform could lead to
Improved and timely diagnosis
Improved patient management
Increased life expectancy
Encourage collaboration
Safes cost of travelling to see other experts

5. Work done during the Hackfest
1: Installed futuregateway API
2. Installed Ophidia
3. Installed and configured a medical image analysis tool – FSL
4. Developed the pipeline to process brain MRI images
a. dicom to analyze converter using dicom_convert
b. brain extraction using FSL
c. registration of one image to another using FSL
d. segmentation using FSL
5. Started the development for Medical Image Analyser- Liferay
6. Registered to use OAR repository

6. Results- Repository using OAR

7. Results- Repository using OAR

8. Results – Interface using Liferay

9. Future plans Before September 5th 2016
1: Connect the interface with the backend liferay
2. Improve on the interface to allow multiple image processing steps
3. Develop a repository using glibrary and or oneData
4. Include segmentation of subcortical brain structures
After September 5th 2016
Get funding and postdoc for full implementation or get a
PhD student for full implementation
a. Include Voxel Based Morphometry for Brain MRI
b. Include other types of images
c. Include other anatomies
d. Include images from all over Africa

10. Summary and Conclusions
The Hackfest has been a unique experience
Science gateway tools were introduced to us
E.g. INDIGO, Ophidia, OAR, Liferay, eLibrary, etc
Opportunity to discuss my use case with experts
Opportunity to use the tools and facilities of Catania University
Started the implementation of my Use case
The future is bright for MIA – Medical Image Analyzer

11. Appreciations
On behalf of all the African participants, I would love to say a big thank you to the meeting organizers, resource persons and support staff
Organizers
Roberto Barbera, sci-gaia
Simon Taylor, sci-gaia
Bruce Becker, sci-gaia
Owen Ivoha, Eko-Konnect
Omo Oaiya, WACREN
Resource Persons
Giacinto Donvito
Riccardo Bruno
Marica Antonacci
Antonio Calanducci
Krzysztof Trzepla
Alessandro D’Anca
Michal Owsiak
Support and Admin staff
Ricardo Bruno
Mario Torrisi (Super!)
Ritta
Marco
We also appreciate the Head of Department of Physics and Astronomy, University of Catania for giving us the space and access to the tools

12. Clockwise: Roberto, Ricardo, Stephen, Diana, David and Benjamin

13. Thank you!
sci-gaia.eu