1. Medical Image Processor and Repository
( MIPAR)
Benjamin Aribisala – Lagos State University - Nigeria

2. Catania- July 2016
The e-Research Summer Hackfest was held at the Department of Physics and Astronomy, University of Catania, Italy
the first edition on July, 4-15, 2016
and the second on July, 18-29, 2016
10 instructors and 36 participants from 9 countries (4 African and 5 European) attended the two editions
co-sponsored by the SCI-GAIA, INDIGO-DataCloud and COST ENeL
The focus of the Hackfest was to train participants on technologies that could help them put their tools on the web as services to users
Participants were trained on the following tools – FutureGateway, gLibrary, Kepler, Invenio, OAI-PMH, OneData and Ophidia

3. Use Cases from Africa TANZANIA 2. NIGERIA 3. KENYA 4. SOUTH AFRICA
Stephen Mgaya, Tanzania Education and Research Network, - Bioinformatics SG (WEKA Data mining tool)
Aron Kondoro, University of Dar es Salaam , iGrid Portal
Diana Rwegasira, University of Dar es Salaam, Technology Transfer Alliance Collaboration Platform
Damas Makweba, Dar es Salaam Institute of Technology, The Weather Research and Forecasting (WRF) Model for the WIMEA-ICT project
Triphonia Ngailo, Dar es Salaam Institute of Technology, The Weather Research and Forecasting (WRF) Model for the WIMEA-ICT project
2. NIGERIA
Benjamin Aribsala, Lagos State University, Medical Image Analyser
3. KENYA
Dennis Muoki Kimego, Egerton University, Public Health Gateway in Kenya
Charles Muiruri Njaramba, Egerton University, Public Health Gateway in Kenya
4. SOUTH AFRICA
David Risinamhodzi, Northwest University, Reproducible Automatic Speech Recognition workflows

4. Lagos Hackfest OBAFEMI AWOLOWO UNIVERSITY 2. COVENANT UNIVERSITY
Segun Oyeyiola, A Near Real-Time Meterological Data Repository for Atmospheric Research in Africa
2. COVENANT UNIVERSITY
Falola Damilare, Development of an interactive pipeline for Genome wide Association
Mosaku Abayomi, IBIS, A Framework For the Interoprability of Bio-repository Information System
Trust Odia, HPC for Large NGS Data: Microbial Diversity Analysis
3. UNIVERSITY OF IBADAN
Olawale Olayide, Valorization of Open Data Archive and Documentation of Research Metadata
4. LAGOS STATE UNIVERSITY
Oluwatoyin Enikuomehin, Web-Based Predictive Defuzzifier
Olusola Olabanjo, MIPAR Extension
5. EDUCATION EDUCATIONAL RESEARCH NETWORK
Yoseph Abate, Education Elibrary and Repository
6. FEDERAL UNIVERSITY OF AGRICULTURE, ABEOKUTA
Olutayo Ajayi, An Adaptive e-Service Communication Model for Rural Agricultural Extension
7. UNIVERSITY OF NSUKKA
Collins Udanor, Development of a SGW-Based Plant Tissue Culture Micropropagation Yield Forecasting Application, Plantisc2

5. Medical Image Processor and Repository

6. Background Medical images are images acquired from humans or animals
Medical images are used for clinical diagnosis, treatment and patient management.
There are many methods of acquiring medical images. Each method has specific use, strengths or weaknesses
Medical Image analysis and computer vision provides a platform for developing computational techniques for converting the raw images to meaningful information.

7. Scientific Problem
Some of the challenges in the field of medical image analysis
Imaging equipment are very expensive
Image acquisition is very expensive
There are limited availability of medical image analysts in Africa
Limited collaboration efforts and ability to share expertise amongst clinical experts
The advancements in internet technology, data communication and reduction in hardware cost has led to the birth of Science Gateway
Science Gateway can help in solving medical image analysis problems by offering tools for
Creating of image repository
Making image analysis tools available
Making workflow available
Adapting some of the tools to make them intelligent
Science Gateway is in top gear in the developed world but very sluggish in Africa
In particular, there is no platform for image analysis in Africa

8. Medical Image Processor and Repository
Medical Image Processor and Repository (MIPAR) is an e-infrastructure for sharing and analyzing medical images
The web address of MIPAR is
MIPAR is one of the products of the collaboration between Lagos State University and SCI-GAIA
For More information, contact us at

9. When Can I Use MIPAR? You need MIPAR if you
need medical images for your research
have medical images to share
have a case study to share
need an expert to process your medical images
How much will you pay for any of the services above?
Everything is free
I want to collaborate with your team
Just send an to

10. System Analysis and Design
Donate Images
Process Images
Download outputs
Download Free Images
Registered user
Analyze Images
Image Types CT
MRI
Doppler
Ultrasound
Anatomy
Brain
Liver
Lung
Chest
Image Format
.hdr/.img
.nii
.nii.gz
(.zip)
Processes
Brain Extraction
Image Segmentation
Image registration

11. System Requirements Software Tools Used for Development
Futuregateway
OAR
PHP
JSON
WAMP
Software Requirement for users
Web browser
Internet
Windows operating system or mac
Hardware Requirement for users
Pentium 4, 4GB RAM, 500 GB disk space

12. Modules of MIPAR Registration Process Analyze Donate Images
Download Images
Process
Images

13. Medical Image Processor and Repository
Home Page

14. Access through Federated Identity
Choose catch-all if in doubt

15. Registration using Federated Identity

16. MIPAR – Image donation (https://mipar.sci-gaia.eu)

17. MIPAR – Image search & download

18. MIPAR – Image search & download & visualise

19. MIPAR – Image processing (brain extraction, segmentation, etc.)

20. MIPAR – Processed Images (e.g. brain extraction and segmentation)

21. Analyze Module Perform Regression Compute correlation
Compare two groups within a dataset
Compare two measurements within a dataset

22. Future Plans and Conclusions
We are currently seeking funds to:
publicize MIPAR
get data into MIPAR
MIPAR was tested with Brain MRI Data,
we need to include other imaging modalities
We also need to include other anatomies
Catania Hackfest was very productive
Opportunity to learn about Science gateway tools
Gave Birth to MIPAR and to Lagos Hackfest
With MIPAR you can share, process and analyse medical images
Conclusions

23. The Team Appreciations
A big appreciation to the co-funders - SCI-GAIA, INDIGO-DATACLOUD AND ENEL
We appreciate Eko-Konnect and WACREN for establishing a link between Lagos State University and SCI-GAIA
The Team
Roberto Barbera, sci-gaia
Simon Taylor, sci-gaia
Benjamin Aribisala
Bruce Becker, sci-gaia
Olabanjo Olusola
Mario Torris
Rita Ricceri
Riccardo Bruno