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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

(a) (b) Joaquín Torres García

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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

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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

• Tools for prevention

risk factors

• Tools for early detection

applicable - acceptable – efficient

• Personalized Treatments

predictive and prognostic tools Data Quality and Quantity from Biomedical Sciences to Clinical Research: Dr Bettina Müller, Medical Oncologist – National Caner Institute, Executive Director - GOCCHI

OpenClinica / BSI server in Chile

• Conectivity
• Speed
• Security

… Clinical Studies

Primary Server (F-Med, University Hospital) BACKUP Server s & HPC) 10 Gb San José Luis Tisné Barros Luco San Borja 100Mb 10 Gb Nat Public Health Nat Cancer Institue 10Mb

Adapted from Dr. J Gomez

Basic Science FONDECYT CONICYT Basic Science ICM R&D FONDEF CONICYT Human Capital Formation Medical Informatics DAAD / DFG 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

United States-Latin America Cancer Research Network, US-LA CRN 2013-2014: U-Redes BioMed-HPC: Network for High Performance Computing 2013-2014: Initiative for Big-Data-Management, Processing, and Distribution for Science and Education in R&D FONDEFS, U-Chile, BNI, F-Med, ICBM, REUNA, …

Basic Science FONDECYT CONICYT Basic Science ICM R&D FONDEF CONICYT Human Capital Formation Medical Informatics DAAD / DFG

Leica TCS LSI: Super Zoom Confocal + SOFI NanoZoomer: Tissue Imaging Perkin Elmer Spinning Disk

TB of Data per Experim ent

Keller et al, Science 322, 2008 Pulgar, Concha, Keller 2012 unpublished

Tens of TB of Data

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

vvv ... Im ... Image P e Processing O Onlin line, iP iPol l @ w @ www.ipo .ipol.im

iP iPol 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

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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 ... ... vvv ... Image Processing Online: iPol @ www.ipol.im

Cross correlation functions

Colocalization 2012 PLosOne 2011 JBC 2011 Arthritis & Rheumatism 2011 Biol Research 2011 Antioxid Redox Signal 2010 Journal of Microscopy …

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 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 …

IPOL

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).

Summer School for High School Students First Year Medical School Students

Poster Rodrigo Rojas (cand PhD): Topological Invariants for Segmentation of Nuclei and Membranes in Breast Cancer Analysis Raquel Pezoa (cand PhD): A segmentation method for images with subjective contours in the field of digital pathology

Professional Development for High School Teachers 'Nervous Tissue: Interactive Practical Activity' Summer School for High School Students ‘Basic Tissues of the Organism' First Year Medical School Students 'Interactive Histology'

Poster Dra Eugenia Diaz: Virtual Microscopy for Professional Development and University Education in Chile

Kothari S, et al. J Am Med Inform Assoc 2013;20:1099–1108

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Optics, Forces & Development Advanced Microscopy and Image Processing

2013 13  Sympos posium um & & Cur urses  2014 14

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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