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Machine Learning for Medical Image Analysis: What, where and how?

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A great career advice for EECS (Electrical, electronics and computer science) graduates interested in machine vision and some advice for a PhD career in Medical Image Analysis.

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Machine Learning for Medical Image Analysis: What, where and how?

  1. 1. Machine Learning for Medical Image Analysis: What, where and how? Dr. Debdoot Sheet Assistant Professor Department of Electrical Engineering Indian Institute of Technology Kharagpur www.facweb.iitkgp.ernet.in/~debdoot/
  2. 2. A GREAT PIECE OF CAREER ADVICE FOR EECS GRADUATES INTERESTED IN MACHINE VISION 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 2
  3. 3. Market Scenario and Career Media, surveillance, automotive, graphics, etc. ($ 6 Billion) 63% Medical Image Analysis ($ 3.5 Billion) 37% Market for Machine Vision Systems in 2020 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 3 Modality • X-ray • Ultrasound • Computed Tomography (CT) • Magnetic Resonance (MRI) • Nuclear Imaging (PET & SPECT) Clinical Indications • Radiology • Cardiology • Oncology • Neurology • Obstetrics & gynecology • Breast mammography End Users • Hospitals • Diagnostic centers • Research centers Report code: HIT 1309 and SE 2701 from www.marketsandmarkets.com
  4. 4. Medical Image Analysis (MedIA)? • Is not Medical Imaging • Is not Medicine • Is not Image Processing • Is not Computer Vision • Is not Machine Learning • Is not Software Engineering • Is not Project Management • Is not Creating Enterprises 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 4
  5. 5. Overview of MedIA 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 5
  6. 6. Last 35 years of MedIA • Pre 1980 – 1984: Era of Pattern Recognition Analysis of 2D Images • 1985 – 1991: Knowledge based Approaches • 1992 – 1998: 3D Images and Towards Integrated Analysis • 1999 – 2010: Machine Learning with Shallow Reasoning • 2010 and Beyond: Machine Learning with Complex Reasoning 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 6 Duncan, J.S.; Ayache, N., "Medical image analysis: progress over two decades and the challenges ahead," IEEE Trans. Pat. Anal., Mach. Intell., vol.22, no.1, pp.85,106, Jan. 2000
  7. 7. Key Research (Business) Areas • Macro - meso - micro imaging • Medical image registration • Organ localization • Organ segmentation • Medical visualization and Augmented reality • Virtual anatomy • Digital angiography • Optical and ultrasonic despeckling • 3D optical microscopy • Digital pathology • Computational imaging 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 7
  8. 8. End use of MedIA 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 8 Tong, S.; Sheet, D.; Bhuiyan, S.; Zequer Diaz, M.; Taberne, A., "BME Trends Around the World : From Baby X to frugal technologies, here's what biomedical engineers are excited about in 2015. [From the Editors]," IEEE Pulse, vol.6, no.1, pp.4-6, Jan.-Feb. 2015
  9. 9. MedIA Challenges in 2015 • Endoscopic vision for Computer Assisted Intervention (CAI) • Statistical shape modeling • Liver ultrasound tracking • Gland segmentation in histology • Retinal cyst segmentation 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 9
  10. 10. MedIA Challenges in 2015 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 10
  11. 11. CAREER ADVICES FOR MedIA PHD ASPIRANTS 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 11
  12. 12. Find a (Research) Challenge • Grand Challenges in Biomedical Image Analysis – www.grand-challenges.org • MICCAI – www.miccai.org – www.miccai2015.org • ISBI – www. biomedicalimaging.org • SPIE Medical Imaging – 2015 will host a grand-challenge 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 12
  13. 13. Tool(boxes) of the Trade • BioDigital Human – www.biodigital.com • MeVisLab – Medical image processing, analysis and visualization SDK – http://www.mevislab.de/ • Python (x,y) – Python 2.7 with scientific computing library for custom building tools – https://code.google.com/p/pythonxy/ • Tortoise SVN – Version control for managing large file software projects – www.tortoisesvn.net/ • MicroDicomViewer – Standalone Viewer for Dicom files – www.microdicom.com/downloads.html • CUDA – Library for using NVIDIA GPUs 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 13
  14. 14. Where to Read for MedIA? Specialist Literature • Medical Image Analysis • IEEE Trans. Medical Imaging • IEEE Trans. Computational Imaging • IEEE J. Biomedical and Health Informatics • SPIE J. Medical Imaging • Computerized Medical Imaging and Graphics General Reading • IEEE Trans. Image Processing • IEEE Trans. Biomedical Engineering • Int. J. Computer Vision • IET Image Processing • IET Computer Vision • ACM Trans. Graphics • Proc. Int. Conf. Image. Proc. 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 14
  15. 15. Where to Read for ML? Journal • IEEE Trans. Pattern Analysis and Machine Intelligence • Machine Learning • J. Machine Learning Research • IEEE Trans. Knowledge and Data Engineering • IEEE Trans. Neural Networks • IEEE Trans. Sys. Man. Cyber. Conferences • Computer Vision and Pattern Recognition (CVPR) • Machine Learning confs. – International (ICML) – European (ECML) – Asian (ACML) • Neural Information Processing System (NIPS) • Computer Vision conf. – International (ICCV) – European (ECCV) – Asian (ACCV) 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 15
  16. 16. Where to Listen and Socialize? Workshops and Schools • Medical Imaging Summer School (MISS) – MICCAI Society • IEEE SPS Summer School on Biomedical Image Analysis – IEEE Signal Processing Soc. • IEEE EMBS Int. Summer School on Biomedical Imaging – IEEE Engineering in Medicine and Biology Society • Biomedical Image Analysis Summer School Conferences • Medical Image Computing and Computer Assisted Intervention (MICCAI) • Int. Symp. Biomed. Imaging (ISBI) • SPIE Med. Imaging • Information Processing in Medical Imaging (IPMI) • Information Processing in Computer-Assisted Interventions (IPCAI) • Microscopy Conference (MC) • Int. Conf. Sys., Med. Biol. (ICSMB) – In IIT Kharagpur, Jan 2016 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 16
  17. 17. Some of the (BIG Group) Leaders • Alejandro Frangi (Sheffield) • Alison Noble (Oxford) • Badrinath Roysam (Houston) • Ben Glocker (Imperial) • Bram van Ginneken (Nijmegen) • Gabor Fichtinger (Queens) • James Duncan (Yale) • Michael Unser (EPFL) • Michael Liebling (UCSB) • Milan Sonka (Iowa) • Nassir Navab (TUM+JHU) • Nicholas Ayache (INRIA Sophia Antipolis Cedex) • Pierre Jannin (INRIA Rennes) • Polina Golland (MIT) • Terry Peters (Robarts) • Wiro Nissen (Erasmus MC) 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 17 Biomedical Imaging and Graphics
  18. 18. Where to Publish? Conferences (Early Track) • MICCAI • ISBI • SPIE Medical Imaging • IPCAI • IPMI • CVPR • ICCV / ECCV / ACCV • ICIP Journal (Mature) • Medical Image Analysis • IEEE Trans. Med. Imaging • IEEE J. Biomed. Health Inf. • IEEE Trans. Biomed. Engg. • Comp. Med. Imag. Graph. • SPIE Med. Imaging • BMC Medical Imaging • Int. J. Biomed. Imaging 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 18
  19. 19. Where to Look for (Creating) Jobs? Incubation, Startup Grants • Technology Business Incubation (TBI) – DSIR – Promoting Innovations in Individuals, Start-ups and MSMEs (PRISM) • Cat I – Rs. 5 lcs (Idea pitchup) • Cat II – Rs. 5-35 lcs (Tech. Demonstrator) • Biotechnology Industry Research Assistance Council (BIRAC) – Biotechnology Ignition Grant (BIG) • Rs. 50 lcs (Tech. Demonstrator) • Indo-US Science and Technology Forum (IUSSTF) – India+US Tech. Starter Endowment • $ 400,000 (Rs. 2.5 Cr) Investments • Mix of Loan + Grant-in-Aid – BIRAC + Department of Electronics and Information Technology (DEITY) • Success of BIG • 50% Grant to University + 50% loan to Start-up • Rs. 3 Cr. (Tech. Commercialization) • Angels and Investors – India Angels Network – Khosla Ventures – Tata Ventures – The Indus Entrepreneurs (TiE) – Corporate Buy-outs 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 19
  20. 20. Take home message Some Texts • Toennies, Guide to medical image analysis, 2012. • Bankman, Handbook of Medical Image Processing and Analysis, 2012. • Dougherty, Medical Image Processing techniques and applications, 2013. • M. N. Gurcan, "Histopathological Image Analysis: A Review", IEEE Rev. Biomed. Engg., vol. 2, pp. 147-171, 2009. • J. A. Noble, “Ultrasound Image Segmentation: A Survey”, IEEE Trans. Med. Imaging, vol. 25, no. 8, pp. 987-1010, 2006. MedIA in Classroom • IIT Kharagpur: http://www.bit.do/eemia • IIT Bombay: http://www.cse.iitb.ac.in/~su yash/cs736/ • Carnegie Mellon: http://www.cs.cmu.edu/~gal eotti/methods_course/ • TU Munich: http://campar.in.tum.de/Cha ir/TeachingWiSe2014CAMP ONE 24 June 2015 Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 20

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