From From Mic Micros roscop opy, y, Ima Imaging to ging to Joaquín Torres García Clinic linical Re l Researc rch: h: A A Latin tin Ame meric rican n Pers rspectiv ive Steffe effen Härte rtel www.scian.cl Laboratory of Scientific Image Analysis (SCIAN-Lab) Biomedical Neuroscience Institute (BNI) Institute of Biomedical Sciences (ICBM) Anatomy and Developmental Biology Program, ICBM, Faculty of Medicine, (a) (b) University of Chile
How ow to to Survive urvive in in the the C Chil hilean n Jungle ungle Steffe effen Härte rtel www.scian.cl Laboratory of Scientific Image Analysis (SCIAN-Lab) Biomedical Neuroscience Institute (BNI) Institute of Biomedical Sciences (ICBM) Anatomy and Developmental Biology Program, ICBM, Faculty of Medicine, University of Chile
How ow to to Survive urvive in the in the Chilean ean Jungle ungle Tis issue ue Steffe effen Härte rtel www.scian.cl Laboratory of Scientific Image Analysis (SCIAN-Lab) Biomedical Neuroscience Institute (BNI) Institute of Biomedical Sciences (ICBM) Anatomy and Developmental Biology Program, ICBM, Faculty of Medicine, University of Chile
Research & Development as % of Gross Domestic Product GDP
R&D as % of gross domestic product GDP Rosvall and Bergstrom, PNAS, 2008
Gross Domestic Product GDP
GDP Density J Gallup, J Sachs and A Mellinger, 1999, International Regional Science Review … "GDP density“: multiplying GDP per capita by the number of people per square km.
Government Dept as % of Gross Domestic Product GDP
Very Large Telescope (VLT), 4 telescopes, 8m, 2600 m Atacama Large Millimeter/submillimeter Array (ALMA), 66 antenna, 5000 m E-ELT European Extremely Large Telescope, 39 m
Extraterrestrial Monster Science produces: TeraB, PetaB, ExaB, ZettaB, YottaB
Data Quality and Quantity from Biomedical Sciences to Clinical Research: Dr Bettina Müller, Medical Oncologist – National Caner Institute, Executive Director - GOCCHI • Tools for prevention risk factors • Tools for early detection applicable - acceptable – efficient • Personalized Treatments predictive and prognostic tools
Nat Public Nat Cancer San Borja San José Luis Tisné Barros Luco Health Institue 10Mb OpenClinica / BSI server in Chile Primary Server (F-Med, University BACKUP Server s & HPC) Hospital) 100Mb - Conectivity - Speed - Security 10 Gb … Clinical Studies 10 Gb
Adapted from Dr. J Gomez
Basic Science R&D Human Capital Formation Basic Science Medical Informatics FONDECYT FONDEF DAAD / DFG ICM CONICYT CONICYT SCIAN-Lab Members ● PI Biophysics ●●●● PostDocs Biology / Computer Sc / Electric Engineer ●●●● PhD - students Computer Sc / Electric Engineer / Biology ●● Master - students Medical Technology / Electric Engineer ● Undergraduate Computer Sc ●●●●● Research – Assistants Medicine / Computer Sc / Electrical Engineer / Biology ●●● Technicians Biotechnology / Labtechnician / Administration
Basic Science R&D Human Capital Formation Basic Science Medical Informatics FONDECYT FONDEF DAAD / DFG ICM CONICYT CONICYT 2013-2014: U-Redes BioMed-HPC: Network for High Performance Computing 2013-2014: Initiative for Big-Data-Management, United States-Latin America Cancer Processing, and Distribution for Science and Research Network, US-LA CRN Education in R&D FONDEFS, U-Chile, BNI, F-Med, ICBM, REUNA, …
Perkin Elmer Spinning Disk Leica TCS LSI: Super Zoom Confocal + SOFI TB of Data per Experim ent NanoZoomer: Tissue Imaging
Pulgar, Concha, Keller 2012 unpublished Tens of TB of Data Keller et al, Science 322, 2008
... Image P ... Im e Processing O Onlin line, iP iPol l vvv @ w @ www.ipo .ipol.im IPOL publishes image processing algorithms as precise and comprehensive as possible. The publication of each algorithm includes: - detailed description, bibliography, commented examples and a failure case analysis - on line demo site for testing of user data - downloadable program in C or C+ + - discussion forum on the algorithm
... Image Processing Online: vvv iPol @ www.ipol.im iPol iP l - La Latin in A America (iP (iPol - LA): ): finan anced b by y CLAR ARA/REUNA f fro rom June 2 2011 11 – Ju July ly 2 201 012 Orga gani nisati tion a n and nd Coo oordinati tion: n: Jua uan n Cardelino no / / Haldo S Spontó ontón Ud n UdelaR ( (Uy Uy) Partic icipa patio ion: : UBA A (Arg rg) ) U-Chile ile (Ch) ) I INAO AOEP EP (Mx) ) U Udela laR (Uy) y) U UC (Uy) y) ... Missi sion on: Diffusion o Dif of iP iPol phil l philosophy a and coll llaboration b bet etween een groups in in LA and w www... ... Edit itoria ial B l Board rd: JM JM Morel el G G Sapi piro S S Osher B Jä B Jähn hne G G R Randall l ... ...
Partial differential equations 2 D/ 3 D · Morpho-topology 2013 Development 2012 European Biophysics Journal 2011 J Microbiol Methods 2010 J of Struct Biol 2010 Development 2010 Biological research 2010 BBA … Motion estim ation and tracking 2014 Current Molecular Medicine IPOL 2013 IPOL 2013 IEEE Transactions on Pattern Analysis … 2013 Biological Cybernetics 2013 Reproduction, Fertility and Development 2012 Machine Vision and Applications 2012 PLosOne 2011 Revista Médica de Chile … Cross correlation functions Colocalization 2012 PLosOne 2011 JBC 2011 Arthritis & Rheumatism 2011 Biol Research 2011 Antioxid Redox Signal 2010 Journal of Microscopy …
Center for Internet Assisted Sperm Analysis CEDAI cuantifies : i. concentration, ii. m otility, iii. vitality, iv. DNA fragm entacion, v. m orphology. w ith m athem atical algoritm s calibrated and standardized by national experts .
Center for Internet Assisted Sperm Analysis
Proyecto D11I1096 I+D precompetitivo CENTRO DE PATOLOGÍA DIGITAL ASISTIDA POR INTERNET XIX Concurso de Proyectos FONDEF de I+D 2011
CPD Center of Digital Pathology
Methodology I&D I&D platform for tele-interconsulting . Development of a Software Platform. Quantification of lymphosites in focal regions ( oral pathology ). I&D, clinical validation of image processing algorithms (HE). Quantification of estrogen receptor in hum an m am m alian tissue . I&D, clinical validation of image processing algorithms (IHQ). Quantification of Cerb2 ( I HQ) in hum an m am m alian tissue . I&D, clinical validation of image processing algorithms (IHQ). Quantification of granules in kidney tissue . I&D, clinical validation of image processing algorithms (IF).
Raquel Pezoa (cand PhD): A segmentation method for images with subjective contours in the field of digital pathology Summer School First Year for High School Medical School Students Students Poster Rodrigo Rojas (cand PhD): Topological Invariants for Segmentation of Nuclei and Membranes in Breast Cancer Analysis
Poster Dra Eugenia Diaz: Virtual Microscopy for Professional Development and University Education in Chile Professional Summer School First Year Development for High School Medical School for High School Students Students Teachers 'Interactive 'Nervous Tissue: ‘Basic Tissues of the Histology' Organism' Interactive Practical Activity'
Kothari S, et al. J Am Med Inform Assoc 2013;20:1099–1108
• Huma uman n and nd Da Data ta Ne Netw twork ork ? ? Ok k ! • Ins Instrume trument nt ? ? Ok k ! • Wh Which ch sof oftw tware re … … sta tand ndard rds/qua quality? lity? Bla lack k box box deve velo lopme ment nt ? • Wha hat t convinc onvinces the the p pathol tholog ogist and nd the the d deve velo loper ? • How ow to to inte integr grate te into into the the workf orkflow lows ? ?
2013 13 Sympos posium um & & Cur urses 2014 14 vvv Physical Biology Optics, Forces & Development of the Cell cellmorphodynamics.cl Advanced Microscopy and Image Processing Computational Bio-Medicine
Th Than ank you you ve very ry muc much Muc Mucha has Graci acias as Vi Vielen en Dan Dank どうもありがとうございました
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