Xiaohong Gao (Middlesex University) – MIRAGE 2011 (developing an embedding visualization toolkit (for 3D images) and a plug-in for uploading queries)

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This document summarizes work on the MIRAGE medical image repository project. It discusses (1) the founding of a new related FP7 project called WIDTH, (2) disseminating research results at conferences, (3) expanding the project team to include students working on image classification and retrieval, and (4) upcoming work digesting medical video data and conducting user evaluations. Technical details are provided on adopting the ParaView platform for 3D image retrieval and developing interfaces for image uploading and wallpaper retrieval.

JISC MIRAGE 2011: RepoFringe 2011 August 4, 2011 Xiaohong (Sharon) Gao Yu (Jade) Qian Middlesex University London NW4 4BT Repository @ http://image.mdx.ac.uk/vin/demo.php.

Demo + Technical details,[object Object]

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http://ganymed.imib.rwth-aachen.de/irma/index_en.php,[object Object]

JISC JISC 1. Project communication (5) - Semantic-based repository: ,[object Object],- http://www.medas.gr:8084/iscore

JISC 2. Disseminations X. Gao, Y, Qian, R. Hui, The State of the Art of Medical Imaging Technology: from Creation to Archive and Back, The Open Medical Informatics Journal, 5 : 93-85, 2011. Y. Qian, X. Gao , M. Loomes, R. Comley, B. Barn, R. Hui, Z. Tian,Content-based Retrieval of 3D Medical Images,eTELEMED2011, February, 2011. (Best paper award, has been invited to be extended to a journal paper by August 15). 3. X.W., Gao, Y. Qian, M. Loomes, R. Comley, B. Barn, A. Chapman, J. Rix, Texture-based 3D image retrieval for medical applications, IADIS e-Health2010, Freiburg, Germany, 29-31, July 2010.

JISC 3. Enlarged Project Team Two BioMed MSc students are working with us doing their final dissertations based on MRIAGE database. ,[object Object]

Working on user studies.2. One PhD student working on Path planning for neurosurgery. ,[object Object],[object Object]

JISC 5. Next stage of work 1. Digest 2D/3D Movie data. 2. User evaluations. 3. Reporting. UltrasonixTABLET Ultrasound scanner MDX Grid Computing

JISC 6. Summary From students’ point of view, this repository has widened both their expectations and experiences, helping them to a large extent. For us, the developers, it has been a great experience.

JISC 7. MIRAGE (Middlesex medical Image Repository with a CBIR ArchivinGEnvironment) ,[object Object],1)Middlesex medical image Repository: 100,000 2D images and 100 3D images 2) CBIR archiving environment: GIFTframework ,[object Object], 1) 3D viewer 2) Upload images Framework of MIRAGE:

Bioinformatics and pathology are obvious scientific partners. Bioinformatics often takes places at the most basic (almost chemical, or even physical) level of life, but much of its procedures to obtain data are destructive. Pathology on the other hand takes place at a much more coarse level of data acquisition (usually where the physical properties of visible light end), but has the advantage of being rooted in the tradition of medicine. The traditional paradigm of pathology is "tissue is the issue". Morphology (exactly the component that often gets overlooked in bioinformatics) plays a large role and helps millions of patients each year around the world. Pathology is proven technology, bioinformatics is limited to niche applications. With the development of whole slide imaging technology some twenty years ago, digital pathology became possible. Observations that used to be for the eyes of the pathologist only, could now be captured and translated into high-resolution pixels, and studied by and communicated to many. Many began to dream of automated tissue evaluation systems and AI-pathology, some even going as far as to suggest the replacement of the pathologist by intelligent computer systems. Meanwhile in several areas of bioinformatics, new limits are being hit. Yes, we can do high-throughput experiments, but noisy datasets are often the results, (inter- and even intra-observer) replicability is difficult, and statistics only offer limited relief. The goal of this introductory lecture is to highlight the problems as well as opportunities for both fields of study, and how exchange of experiences, and (in a later stadium) integration of techniques close the scientific gap that still exists in a great many areas. There is no lack of pathology-centric workshops that offer insights into the world of algorithms. With the CPW event however, we take another approach. We want to bring together the most advanced groups in digital pathology, with the bioinformatics community, to explore the opportunities that exist on both sides of the fence. We start by explaining the basic data types that are introduced by digital pathology. We also explain where they come from, and why this presents unique challenges when it comes to data mining and image analysis. Finally, we introduce PMA.start, a free software environment that can be used to universally gain access to digital pathology (imaging) data. Bioinformatics groups can help quantify, model, and reduce morphological whole tissue data. Pathologists can help interpret and explain heterogeneous high-throughput datasets. And the first seeds of such collaboration can be planted right here, in Athens.

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Xiaohong Gao (Middlesex University) – MIRAGE 2011 (developing an embedding visualization toolkit (for 3D images) and a plug-in for uploading queries)

1. JISC MIRAGE 2011: RepoFringe 2011 August 4, 2011 Xiaohong (Sharon) Gao Yu (Jade) Qian Middlesex University London NW4 4BT Repository @ http://image.mdx.ac.uk/vin/demo.php.

3. Dissemination

4. Progress so far

5. Next stage of work

6. Summary

8. WIDTH – Warehousing images in the digital hospital: interpretation, infrastructure, and integration.

9. Funding Scheme – staff exchange

10.

11.

12.

13. JISC 2. Disseminations X. Gao, Y, Qian, R. Hui, The State of the Art of Medical Imaging Technology: from Creation to Archive and Back, The Open Medical Informatics Journal, 5 : 93-85, 2011. Y. Qian, X. Gao , M. Loomes, R. Comley, B. Barn, R. Hui, Z. Tian,Content-based Retrieval of 3D Medical Images,eTELEMED2011, February, 2011. (Best paper award, has been invited to be extended to a journal paper by August 15). 3. X.W., Gao, Y. Qian, M. Loomes, R. Comley, B. Barn, A. Chapman, J. Rix, Texture-based 3D image retrieval for medical applications, IADIS e-Health2010, Freiburg, Germany, 29-31, July 2010.

14.

15.

16. JISC 4. Uploading images (2)

17. JISC 5. Next stage of work 1. Digest 2D/3D Movie data. 2. User evaluations. 3. Reporting. UltrasonixTABLET Ultrasound scanner MDX Grid Computing

18. JISC 6. Summary From students’ point of view, this repository has widened both their expectations and experiences, helping them to a large extent. For us, the developers, it has been a great experience.

19. JISC Technical Aspects of MIRAGE

20.

21. JISC JISC 8. 3D Image retrieval (1) - interface Montage MIRAGE MIRAGE 2011

22.

23. JISC 9. Image upload(1) - interface MIRAGE MIRAGE2011

24. JISC 9. Image upload(2) – framework of query by upload image

25. JISC JISC 10: MIRAGE system for wallpaper image retrieval

26. JISC

Xiaohong Gao (Middlesex University) – MIRAGE 2011 (developing an embedding visualization toolkit (for 3D images) and a plug-in for uploading queries)

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