Post on 08-Aug-2015
Machine Learning for Medical Image Analysis:
What, where and how?
Dr. Debdoot SheetAssistant Professor
Department of Electrical EngineeringIndian Institute of Technology Kharagpur
www.facweb.iitkgp.ernet.in/~debdoot/
Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 2
A GREAT PIECE OF CAREER ADVICE FOR EECS GRADUATES INTERESTED IN MACHINE VISION
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Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 3
Market Scenario and Career
Media, surveillance, automotive, graphics,
etc.($ 6 Billion)63%
Medical Image Ana-lysis
($ 3.5 Billion)37%
Market for Machine Vision Systems in 2020
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Modality• X-ray• Ultrasound• Computed Tomography
(CT)• Magnetic Resonance (MRI)• Nuclear Imaging (PET &
SPECT)Clinical Indications• Radiology• Cardiology• Oncology• Neurology• Obstetrics & gynecology• Breast mammographyEnd Users• Hospitals• Diagnostic centers• Research centersReport code: HIT 1309 and SE 2701 from www.marketsandmarkets.com
Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 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 Enterprises24 June 2015
Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 5
Overview of MedIA
• Prediction• Example based
learning• Complex
reasoning
• Denoising• Segmentation• Feature
representation• Visualization
• Tissue-energy interaction
• Image formation• Statistics
• Modalities – CT, MRI, US, Microscopy, OCT
• Organ appearance
Medical ImagingPhysics
Machine LearningImage
Processing and
Graphics
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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
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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
Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 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
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End use of MedIA
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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
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MedIA Challenges in 2015• Endoscopic vision for
Computer Assisted Intervention (CAI)
• Statistical shape modeling
• Liver ultrasound tracking
• Gland segmentation in histology
• Retinal cyst segmentation
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MedIA Challenges in 2015
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www.gra
nd-chall
enges.o
rg
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CAREER ADVICES FOR MedIA PHD ASPIRANTS
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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
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Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 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
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Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 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 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)
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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
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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
Biomedical Imaging and Graphics
Intro to Machine Learning for Medical Image Analysis [Debdoot Sheet] - WMLMIA 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
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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
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Take home messageSome 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/~suyash/cs736/
• Carnegie Mellon: http://www.cs.cmu.edu/~galeotti/methods_course/
• TU Munich: http://campar.in.tum.de/Chair/TeachingWiSe2014CAMPONE
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