A pretty picture, or a measurement? Retinal Imaging

Size: px
Start display at page:

Download "A pretty picture, or a measurement? Retinal Imaging"

Transcription

1 Big Data Challenges

2 A pretty picture, or a measurement? Organelles Dynamics Cells Retinal Imaging Physiology Pathology

3 Fundus Camera Optical coherence tomography Fluorescence Histology High Content Screening Fluorescence Lifetime Imaging Atomic Force Microscopy Electron Microscopy Dicom from Bio- magnetic Imaging to Ultrasound

4 Overview of types of imaging Objective Data Type Dimensionality Size Analysis Complexity Methods

5 Overview The specimen is illuminated with light of a specific wavelength (or wavelengths) which is absorbed by the fluorophores, causing them to emit light of longer wavelengths (i.e., of a different colour than the absorbed light). The illumination light is separated from the much weaker emitted fluorescence through the use of a spectral emission filter. This emitted light is stored as channels. Multi- colour images of several types of fluorophores must be composed by combining several single- colour images.

6 Detector Ocular Emission Filter Light Source Dichroic Filter Excitation Filter Objective Sample

7 X, Y typically 512x512 or 1024x1024 but now seeing larger(8192x8192). 50Kx50K common in pathology images. Z component microscopes have a depth of focus meaning they can see into a sample by a few microns. Time component Time lapse images are common in cell biology and Fluorescein angiography. Timescale: up to 72 hours. Channel component In fluorescence microscopy proteins can tagged with a dye that fluoresces at a particular wavelength. In AFM microscopy there can be many non- image features recorded. It is typical to have 3-4 channels in an image, though some imaging techniques can have 30+. Bit depth Typically 12 bit, but can be 8, 16,32, float, double or complex

8 Type: 5D Images Data type: typically 8, 12 or 16bit X, Y: 512, 512 now moving on to 4096, 4096 Z: In fixed cell can be 64+, less in live cell imaging T: 0 in fixed cells, can be in live cell imaging C: 3-4 typical, can be more. Size: 8MB- 50GB

9 Pipettes and vials 96/384 well plates and robot control

10

11 Cells Image Data Numerical Data Information

12

13 Type: 5D Images Data type: typically 8, 12 or 16bit X, Y: 512, 512 now moving on to 2048, 2048 Wells: 96, 384, 3840 Z: Commonly only on 1 section T: 0, but recent article in science showing live cell HCS. C: was 1, or2, 3-4 typical, can be more. Size: 1GB- 600GB

14 Performed by examining a thin slice (section) of tissue under a light microscope or electron microscope. The ability to visualize or differentially identify microscopic structures is frequently enhanced through the use of histological stains. Histology is an essential tool of biology and medicine. Biological tissue has little inherent contrast in either the light or electron microscope. Staining is employed to give both contrast to the tissue as well as highlighting particular features of interest.

15 Type: 3D Images Data type: typically 8 bit X, Y: 30K, 30K can be over 100K, 100K Z: Normally 1 z- section, but can br 20+ T: 0, fixed cell imaging C: 2-3 typical, quite often mixed colour rather than pseudo colour. Size: Highly compressed using JPEG2000- often very lossy; uncompressed 10GB- 30GB single plane images.

16 Accurate protocols and efficient algorithms can be run on whole slides or specified areas. Under the control of a pathologist scoring can become more accurate and achieve higher throughput to increase statistical significance. There is currently high interest in cancer biomarker expression quantification. In the research and pharmaceutical industries these methods become increasingly important in proportion to the number of markers, targets, and drugs to test.

17 Digital Acquisition System Image Raw Data Metadata Processed Data Metadata OMERO Quantitative Analysis Metaphase Image for Publication Anaphase Image for Publication Telophase Image for Publication Visualizing Data Management, tagging and querying

18 OMERO DB Image Data Associated Files ICE.grid Hibernate Spring AOP IOC C3PO DB ICE C++ Java Bio- Formats OMERO.editor OMERO.insight OMERO.insight Services Services Services Services OMERO.fs Python OMERO.matlab OMERO.web OMERO.scripts

19 Structure your image data Annotate your analysis results Attach your analysis results Images Datasets Projects Other data

20

21

22 Histology one big image, low compute Pyramid Generation High Content Screening many smaller images, high compute Classification FLIM smaller images, high compute Interactive, curve fitting and model selection

23 Image Data Associated Files OMERO DB Submit node ICE.grid Hibernate Spring AOP IOC C3PO DB Services Services OMERO.fs Services Services ICE C++ Java Python Submit node HPC Service

24 Xml specification held on OMERO server User calls HPC service (which wraps RAPID) with id of xml file and parameters. Rapid submits the job using the xml specification The resulting script runs on the cluster gets the data from OMERO There are two datasets, one for control and one containing the experimental condition. Distributes image via MPI to worker nodes The analysis results are attached to the dataset containing the images with the experimental condition

25 Image generation occurs on OMERO server OMERO server overloaded building image pyramid Short term solution Generate pyramids on cluster Problem Moving data from OMERO to cluster Rendering settings change, rebuild the pyramid

26 Queen's Medical Research Institute Royal Infirmary 500 user site Training Scripts for profiling server configurations Histology data, 200 images/day, new scope z- sections and stains Change colour mapping in realtime Interactive analysis of ROI. Leveraging analysis

MICROSCOPY DAY 2011: Understanding and handling image data Martin Spitaler

MICROSCOPY DAY 2011: Understanding and handling image data Martin Spitaler Imperial College London Understanding and handling image data Understanding Images () What s in an image file: Pixel data metadata Getting the data into the file: Image acquisition Image file formats Using

More information

Euro-BioImaging European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences

Euro-BioImaging European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences Euro-BioImaging European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences WP11 Data Storage and Analysis Task 11.1 Coordination Deliverable 11.2 Community Needs of

More information

Euro-BioImaging European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences

Euro-BioImaging European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences Euro-BioImaging European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences WP11 Data Storage and Analysis Task 11.1 Coordination Deliverable 11.3 Selected Standards

More information

DMBI: Data Management for Bio-Imaging.

DMBI: Data Management for Bio-Imaging. DMBI: Data Management for Bio-Imaging. Questionnaire Data Report 1.0 Overview As part of the DMBI project an international meeting was organized around the project to bring together the bio-imaging community

More information

Safe Software Standards and XML Schemas

Safe Software Standards and XML Schemas Copyright 2010 Society of Photo-Optical Instrumentation Engineers. This paper will be published in SPIE BIOS Proceeding Volume 7556 and is made available as an electronic preprint with permission of SPIE.

More information

DICOM in Pathology. 2005 DICOM International Conference Budapest, Hungary

DICOM in Pathology. 2005 DICOM International Conference Budapest, Hungary DICOM in Pathology 2005 DICOM International Conference Budapest, Hungary Bruce Beckwith, MD Department of Pathology Beth Israel Deaconess Medical Center Harvard Medical School Boston, Massachusetts, USA

More information

MIRAX SCAN The new way of looking at pathology

MIRAX SCAN The new way of looking at pathology Microscopy from Carl Zeiss MIRAX SCAN The new way of looking at pathology Greater reliability. Greater efficiency. Virtual microscopy for research & analysis. Better. More efficient. Quality as the basis

More information

Digital Imaging and Communications in Medicine (DICOM) Supplement 145: Whole Slide Microscopic Image IOD and SOP Classes

Digital Imaging and Communications in Medicine (DICOM) Supplement 145: Whole Slide Microscopic Image IOD and SOP Classes 5 Digital Imaging and Communications in Medicine (DICOM) Supplement 145: Whole Slide Microscopic Image IOD and SOP Classes 10 15 20 Prepared by: DICOM Standards Committee, Working Group 26, Pathology 1300

More information

CHAPTER FIVE RESULT ANALYSIS

CHAPTER FIVE RESULT ANALYSIS CHAPTER FIVE RESULT ANALYSIS 5.1 Chapter Introduction 5.2 Discussion of Results 5.3 Performance Comparisons 5.4 Chapter Summary 61 5.1 Chapter Introduction This chapter outlines the results obtained from

More information

Fluorescent dyes for use with the

Fluorescent dyes for use with the Detection of Multiple Reporter Dyes in Real-time, On-line PCR Analysis with the LightCycler System Gregor Sagner, Cornelia Goldstein, and Rob van Miltenburg Roche Molecular Biochemicals, Penzberg, Germany

More information

Applications of confocal fluorescence microscopy in biological sciences

Applications of confocal fluorescence microscopy in biological sciences Applications of confocal fluorescence microscopy in biological sciences B R Boruah Department of Physics IIT Guwahati Email: brboruah@iitg.ac.in Page 1 Contents Introduction Optical resolution Optical

More information

Fundamentals of Image Analysis and Visualization (the short version) Rebecca Williams, Director, BRC-Imaging

Fundamentals of Image Analysis and Visualization (the short version) Rebecca Williams, Director, BRC-Imaging Fundamentals of Image Analysis and Visualization (the short version) Rebecca Williams, Director, BRC-Imaging A digital image is a matrix of numbers (in this case bytes) 6 2 4 4 2 0 2 0 2 4 4 4 4 8 12 4

More information

Servicio de Salud de Castilla-La Mancha

Servicio de Salud de Castilla-La Mancha Servicio de Salud de Castilla-La Mancha Telepathology network of Castilla-La Mancha MARCIAL GARCÍA ROJO Chief. Pathology Department Hospital General de Ciudad Real marcial@cim.es Servicio de Anatomía Patológica

More information

MI Software. Innovation with Integrity. High Performance Image Analysis and Publication Tools. Preclinical Imaging

MI Software. Innovation with Integrity. High Performance Image Analysis and Publication Tools. Preclinical Imaging MI Software High Performance Image Analysis and Publication Tools Innovation with Integrity Preclinical Imaging Molecular Imaging Software Molecular Imaging (MI) Software provides high performance image

More information

Confocal Microscopy and Atomic Force Microscopy (AFM) A very brief primer...

Confocal Microscopy and Atomic Force Microscopy (AFM) A very brief primer... Confocal Microscopy and Atomic Force Microscopy (AFM) of biofilms A very brief primer... Fundamentals of Confocal Microscopy Based on a conventional fluorescence microscope Fluorescent Microscope Confocal

More information

ParaVision 6. Innovation with Integrity. The Next Generation of MR Acquisition and Processing for Preclinical and Material Research.

ParaVision 6. Innovation with Integrity. The Next Generation of MR Acquisition and Processing for Preclinical and Material Research. ParaVision 6 The Next Generation of MR Acquisition and Processing for Preclinical and Material Research Innovation with Integrity Preclinical MRI A new standard in Preclinical Imaging ParaVision sets a

More information

COMPENSATION MIT Flow Cytometry Core Facility

COMPENSATION MIT Flow Cytometry Core Facility COMPENSATION MIT Flow Cytometry Core Facility Why do we need compensation? 1) Because the long emission spectrum tail of dyes causes overlap like with the fluorophores FITC and PE. 2) For sensitivity reasons,

More information

ZEISS Microscopy Course Catalog

ZEISS Microscopy Course Catalog ZEISS Microscopy Course Catalog ZEISS Training and Education Expand Your Possibilities Practical microscopy training has a long tradition at ZEISS. The first courses were held in Jena as early as 1907,

More information

Technical Considerations Detecting Transparent Materials in Particle Analysis. Michael Horgan

Technical Considerations Detecting Transparent Materials in Particle Analysis. Michael Horgan Technical Considerations Detecting Transparent Materials in Particle Analysis Michael Horgan Who We Are Fluid Imaging Technology Manufacturers of the FlowCam series of particle analyzers FlowCam HQ location

More information

MITOSIS IN ONION ROOT TIP CELLS: AN INTRODUCTION TO LIGHT MICROSCOPY

MITOSIS IN ONION ROOT TIP CELLS: AN INTRODUCTION TO LIGHT MICROSCOPY MITOSIS IN ONION ROOT TIP CELLS: AN INTRODUCTION TO LIGHT MICROSCOPY Adapted from Foundations of Biology I; Lab 6 Introduction to Microscopy Dr. John Robertson, Westminster College Biology Department,

More information

Understanding Digital Modalities: System Integration and Use

Understanding Digital Modalities: System Integration and Use Understanding Digital Modalities: System Integration and Use Donald J. Peck, PhD Henry Ford Health System Detroit, MI donaldp@rad.hfh.edu Dicom Digital Imaging and Communications in Medicine Part 3: Information

More information

Chapter 12 Filters for FISH Imaging

Chapter 12 Filters for FISH Imaging Chapter 12 Filters for FISH Imaging Dan Osborn The application of in situ hybridization (ISH) has advanced from short lived, non-specific isotopic methods, to very specific, long lived, multiple color

More information

Chapter 4. Microscopy, Staining, and Classification. Lecture prepared by Mindy Miller-Kittrell North Carolina State University

Chapter 4. Microscopy, Staining, and Classification. Lecture prepared by Mindy Miller-Kittrell North Carolina State University Chapter 4 Microscopy, Staining, and Classification 2012 Pearson Education Inc. Lecture prepared by Mindy Miller-Kittrell North Carolina State University Microscopy and Staining 2012 Pearson Education Inc.

More information

#jenkinsconf. Jenkins as a Scientific Data and Image Processing Platform. Jenkins User Conference Boston #jenkinsconf

#jenkinsconf. Jenkins as a Scientific Data and Image Processing Platform. Jenkins User Conference Boston #jenkinsconf Jenkins as a Scientific Data and Image Processing Platform Ioannis K. Moutsatsos, Ph.D., M.SE. Novartis Institutes for Biomedical Research www.novartis.com June 18, 2014 #jenkinsconf Life Sciences are

More information

Microscopy. MICROSCOPY Light Electron Tunnelling Atomic Force RESOLVE: => INCREASE CONTRAST BIODIVERSITY I BIOL1051 MAJOR FUNCTIONS OF MICROSCOPES

Microscopy. MICROSCOPY Light Electron Tunnelling Atomic Force RESOLVE: => INCREASE CONTRAST BIODIVERSITY I BIOL1051 MAJOR FUNCTIONS OF MICROSCOPES BIODIVERSITY I BIOL1051 Microscopy Professor Marc C. Lavoie marc.lavoie@cavehill.uwi.edu MAJOR FUNCTIONS OF MICROSCOPES MAGNIFY RESOLVE: => INCREASE CONTRAST Microscopy 1. Eyepieces 2. Diopter adjustment

More information

Zeiss 780 Training Notes

Zeiss 780 Training Notes Zeiss 780 Training Notes 780 Start Up Sequence Do you need the argon laser, 458,488,514nm lines? No Turn on the Systems PC Switch Turn on Main Power Switch Yes Turn on the laser main power switch and turn

More information

Products - Microarray Scanners - SpotLight Two-Color Microarray Fluorescence Scanners New! SpotLight 2 now available!

Products - Microarray Scanners - SpotLight Two-Color Microarray Fluorescence Scanners New! SpotLight 2 now available! Products - Microarray Scanners - SpotLight Two-Color Microarray Fluorescence Scanners New! SpotLight 2 now available! Arrayit SpotLight Two-Color Microarray Scanners provide the market s most affordable

More information

Lecture 20: Scanning Confocal Microscopy (SCM) Rationale for SCM. Principles and major components of SCM. Advantages and major applications of SCM.

Lecture 20: Scanning Confocal Microscopy (SCM) Rationale for SCM. Principles and major components of SCM. Advantages and major applications of SCM. Lecture 20: Scanning Confocal Microscopy (SCM) Rationale for SCM. Principles and major components of SCM. Advantages and major applications of SCM. Some limitations (disadvantages) of NSOM A trade-off

More information

Z-Stacking and Z-Projection using a Scaffold-based 3D Cell Culture Model

Z-Stacking and Z-Projection using a Scaffold-based 3D Cell Culture Model A p p l i c a t i o n N o t e Z-Stacking and Z-Projection using a Scaffold-based 3D Cell Culture Model Brad Larson and Peter Banks, BioTek Instruments, Inc., Winooski, VT Grant Cameron, TAP Biosystems

More information

Health Management Information Systems: Medical Imaging Systems. Slide 1 Welcome to Health Management Information Systems, Medical Imaging Systems.

Health Management Information Systems: Medical Imaging Systems. Slide 1 Welcome to Health Management Information Systems, Medical Imaging Systems. Health Management Information Systems: Medical Imaging Systems Lecture 8 Audio Transcript Slide 1 Welcome to Health Management Information Systems, Medical Imaging Systems. The component, Health Management

More information

Neuro imaging: looking with lasers in the brain

Neuro imaging: looking with lasers in the brain Neuro imaging: looking with lasers in the brain Aim: To image life cells, label free, with cellular resolution in deep tissue Marloes Groot Vrije Universiteit Amsterdam Faculteit Exacte Wetenschappen Natuurkunde

More information

Microscopy: Principles and Advances

Microscopy: Principles and Advances Microscopy: Principles and Advances Chandrashekhar V. Kulkarni University of Central Lancashire, Preston, United kingdom May, 2014 University of Ljubljana Academic Background 2005-2008: PhD-Chemical Biology

More information

Copyright 2011 Penguin Computing, Inc. All rights reserved. Interactive Preclinical Analytics via GPU Cloud Platform

Copyright 2011 Penguin Computing, Inc. All rights reserved. Interactive Preclinical Analytics via GPU Cloud Platform Copyright 2011 Penguin Computing, Inc. All rights reserved Interactive Preclinical Analytics via GPU Cloud Platform Numira and Penguin Partnership Penguin POD Innovative HPC as a Service platform > Strong

More information

Data deluge (and it s applications) Gianluigi Zanetti. Data deluge. (and its applications) Gianluigi Zanetti

Data deluge (and it s applications) Gianluigi Zanetti. Data deluge. (and its applications) Gianluigi Zanetti Data deluge (and its applications) Prologue Data is becoming cheaper and cheaper to produce and store Driving mechanism is parallelism on sensors, storage, computing Data directly produced are complex

More information

DICOM Digital Imaging and Communications in Medicine

DICOM Digital Imaging and Communications in Medicine DICOM Digital Imaging and Communications in Medicine INF5081 / Vårsemester 2007 Wolfgang Leister Reidar Øksnevad Pedro Cruz G. April 2007 PACS PACS = Picture Archive and Communication System Archive for

More information

March 19, 2014. Dear Dr. Duvall, Dr. Hambrick, and Ms. Smith,

March 19, 2014. Dear Dr. Duvall, Dr. Hambrick, and Ms. Smith, Dr. Daniel Duvall, Medical Officer Center for Medicare, Hospital and Ambulatory Policy Group Centers for Medicare and Medicaid Services 7500 Security Boulevard Baltimore, Maryland 21244 Dr. Edith Hambrick,

More information

OPERATING INSTRUCTIONS Nikon TiE Deconvolution Microscope CCRB 1-220G

OPERATING INSTRUCTIONS Nikon TiE Deconvolution Microscope CCRB 1-220G OPERATING INSTRUCTIONS Nikon TiE Deconvolution Microscope CCRB 1-220G Conventions Through these notes bold font refers to a software button and italics refer to a hardware switch. The software makes extensive

More information

DOLPHIN DICOM IMAGING DICOM CONFORMANCE STATEMENT

DOLPHIN DICOM IMAGING DICOM CONFORMANCE STATEMENT DOLPHIN DICOM IMAGING DICOM CONFORMANCE STATEMENT NOTICE The software described in this document has been validated in accordance with the governing DICOM standard at the time of this document's release.

More information

Technical Note. Roche Applied Science. No. LC 19/2004. Color Compensation

Technical Note. Roche Applied Science. No. LC 19/2004. Color Compensation Roche Applied Science Technical Note No. LC 19/2004 Purpose of this Note Color The LightCycler System is able to simultaneously detect and analyze more than one color in each capillary. Due to overlap

More information

Introduction to flow cytometry

Introduction to flow cytometry Introduction to flow cytometry Flow cytometry is a popular laser-based technology. Discover more with our introduction to flow cytometry. Flow cytometry is now a widely used method for analyzing the expression

More information

The Extension of the DICOM Standard to Incorporate Omics

The Extension of the DICOM Standard to Incorporate Omics Imperial College London The Extension of the DICOM Standard to Incorporate Omics Data Richard I Kitney, Vincent Rouilly and Chueh-Loo Poh Department of Bioengineering We stand at the dawn of a new understanding

More information

Cell Cycle in Onion Root Tip Cells (IB)

Cell Cycle in Onion Root Tip Cells (IB) Cell Cycle in Onion Root Tip Cells (IB) A quick overview of cell division The genetic information of plants, animals and other eukaryotic organisms resides in several (or many) individual DNA molecules,

More information

Thermo Scientific ArrayScan XTI High Content Analysis Reader. revolutionizing cell biology with the power of high content

Thermo Scientific ArrayScan XTI High Content Analysis Reader. revolutionizing cell biology with the power of high content Thermo Scientific ArrayScan XTI High Content Analysis Reader revolutionizing cell biology with the power of high content learn more about your cells using high content technology Thermo Scientific High

More information

Distributed Computing and Big Data: Hadoop and MapReduce

Distributed Computing and Big Data: Hadoop and MapReduce Distributed Computing and Big Data: Hadoop and MapReduce Bill Keenan, Director Terry Heinze, Architect Thomson Reuters Research & Development Agenda R&D Overview Hadoop and MapReduce Overview Use Case:

More information

Taking the Confusion out of Confocal Microscopy

Taking the Confusion out of Confocal Microscopy KEYWORDS: confocal microscopy, fluorescence imaging, three dimensional Special section on techniques: Taking the Confusion out of Confocal Microscopy Nana Rezai Pathology, University of British Columbia

More information

Introducing MIPAV. In this chapter...

Introducing MIPAV. In this chapter... 1 Introducing MIPAV In this chapter... Platform independence on page 44 Supported image types on page 45 Visualization of images on page 45 Extensibility with Java plug-ins on page 47 Sampling of MIPAV

More information

These particles have something in common

These particles have something in common These particles have something in common Blood cells Chromosomes Algae Protozoa Certain parameters of these particles can be measured with a flow cytometer Which parameters can be measured? the relative

More information

The best lab standard. 1,4 Megapixels 2/3 inch sensor Giant pixel size 6 times optical zoom Massive 16-bit imaging for enhanced dynamic

The best lab standard. 1,4 Megapixels 2/3 inch sensor Giant pixel size 6 times optical zoom Massive 16-bit imaging for enhanced dynamic 1 AGENDA Product roadmap...3 Computer based system: PLATINUM..5 XPLORER.6 ESSENTIAL..7 Specifications Computer based system..8 Configuration Computer based system... 9 Software Computer based system...10

More information

inform Advanced Image Analysis Software For Accurately Quantifying Biomarkers in Tissue Sections

inform Advanced Image Analysis Software For Accurately Quantifying Biomarkers in Tissue Sections P R O D U C T N O T E inform Advanced Image Analysis Key Features Quantitative analysis of biomarker epression in tissue sections and TMAs Separation of weakly epressing and overlapping markers Cellular

More information

Multispectral stereo acquisition using 2 RGB cameras and color filters: color and disparity accuracy

Multispectral stereo acquisition using 2 RGB cameras and color filters: color and disparity accuracy Multispectral stereo acquisition using 2 RGB cameras and color filters: color and disparity accuracy (a) and Bernhard Hill (b) (a) Institute of Imaging and Computer Vision (b) Research Group Color and

More information

Introduction to Flow Cytometry

Introduction to Flow Cytometry Introduction to Flow Cytometry presented by: Flow Cytometry y Core Facility Biomedical Instrumentation Center Uniformed Services University Topics Covered in this Lecture What is flow cytometry? Flow cytometer

More information

Imaging and Bioinformatics Software

Imaging and Bioinformatics Software Imaging and Bioinformatics Software Software Overview 242 Gel Analysis Software 243 Ordering Information 246 Software Overview Software Overview See Also Imaging systems: pages 232 237. Bio-Plex Manager

More information

VENTANA Digital Pathology. Reliable. Efficient. Comprehensive.

VENTANA Digital Pathology. Reliable. Efficient. Comprehensive. VENTANA Digital Pathology Reliable. Efficient. Comprehensive. In the quest to improve the lives of all patients afflicted with cancer, every second counts. Fast, informed clinical decisions are essential

More information

Basic principles and mechanisms of NSOM; Different scanning modes and systems of NSOM; General applications and advantages of NSOM.

Basic principles and mechanisms of NSOM; Different scanning modes and systems of NSOM; General applications and advantages of NSOM. Lecture 16: Near-field Scanning Optical Microscopy (NSOM) Background of NSOM; Basic principles and mechanisms of NSOM; Basic components of a NSOM; Different scanning modes and systems of NSOM; General

More information

Application of Automated Data Collection to Surface-Enhanced Raman Scattering (SERS)

Application of Automated Data Collection to Surface-Enhanced Raman Scattering (SERS) Application Note: 52020 Application of Automated Data Collection to Surface-Enhanced Raman Scattering (SERS) Timothy O. Deschaines, Ph.D., Thermo Fisher Scientific, Madison, WI, USA Key Words Array Automation

More information

Patient Photographs in the Electronic Health Record

Patient Photographs in the Electronic Health Record Summit on Color in Medical Imaging Silver Spring, MD, USA May 8-9, 2013 Patient Photographs in the Electronic Health Record Michael Flynn Radiology Research Henry Ford Health System Detroit, MI Outline:

More information

Biology 3460 - Plant Physiology - Lab Exercise 2 Basic Lab Techniques

Biology 3460 - Plant Physiology - Lab Exercise 2 Basic Lab Techniques Biol3460 Lab 1 1 Biology 3460 - Plant Physiology - Lab Exercise 2 Basic Lab Techniques Objectives: This lab is intended to: (1) provide an introduction to basic techniques used in biology labs (2) provide

More information

APPLICATION INFORMATION

APPLICATION INFORMATION DRAFT: Rev. D A-2045A APPLICATION INFORMATION Flow Cytometry 3-COLOR COMPENSATION Raquel Cabana,* Mark Cheetham, Jay Enten, Yong Song, Michael Thomas,* and Brendan S. Yee Beckman Coulter, Inc., Miami FL

More information

a measurable difference

a measurable difference Thermo Scientific Cell Analysis Software and Informatics Products a measurable difference for everyone Thermo Scientific HCS Studio Cell Analysis Software Thermo Scientific Store Image and Database Management

More information

Chapter 13 Confocal Laser Scanning Microscopy C. Robert Bagnell, Jr., Ph.D., 2012

Chapter 13 Confocal Laser Scanning Microscopy C. Robert Bagnell, Jr., Ph.D., 2012 Chapter 13 Confocal Laser Scanning Microscopy C. Robert Bagnell, Jr., Ph.D., 2012 You are sitting at your microscope working at high magnification trying to sort out the three-dimensional compartmentalization

More information

Principles of Microscopy and Confocal and Fluorescence Microscopy

Principles of Microscopy and Confocal and Fluorescence Microscopy Principles of Microscopy and Confocal and Fluorescence Microscopy Content This course in Light Microscopy follows the series of successful courses in Light Microscopy, Confocal and Fluorescence Microscopy

More information

White Paper. Zecotek Visible Fiber Laser Platform. Enabling the future of laser technology

White Paper. Zecotek Visible Fiber Laser Platform. Enabling the future of laser technology White Paper Zecotek Visible Fiber Laser Platform Enabling the future of laser technology Zecotek Photonics Inc. (TSX- V: ZMS; Frankfurt: W1I) www.zecotek.com is a Canadian photonics technology company

More information

Using the Grid for the interactive workflow management in biomedicine. Andrea Schenone BIOLAB DIST University of Genova

Using the Grid for the interactive workflow management in biomedicine. Andrea Schenone BIOLAB DIST University of Genova Using the Grid for the interactive workflow management in biomedicine Andrea Schenone BIOLAB DIST University of Genova overview background requirements solution case study results background A multilevel

More information

Laser Ablation Tomography. A Meso-Scale Volumetric Visualization and Analysis Tool

Laser Ablation Tomography. A Meso-Scale Volumetric Visualization and Analysis Tool Laser Ablation Tomography A Meso-Scale Volumetric Visualization and Analysis Tool March 2015 Cover Image: Burning Branch 2015 by L4iS Current Page: Seed with Internal Network 2015 by L4iS All images are

More information

Open & Big Data for Life Imaging Technical aspects : existing solutions, main difficulties. Pierre Mouillard MD

Open & Big Data for Life Imaging Technical aspects : existing solutions, main difficulties. Pierre Mouillard MD Open & Big Data for Life Imaging Technical aspects : existing solutions, main difficulties Pierre Mouillard MD What is Big Data? lots of data more than you can process using common database software and

More information

Phase-Contrast & Fluorescence Microscopy of Adherent Cells grown on ECIS Electrodes

Phase-Contrast & Fluorescence Microscopy of Adherent Cells grown on ECIS Electrodes Phase-Contrast & Fluorescence Microscopy of Adherent Cells grown on ECIS Electrodes Prof. Joachim Wegener University of Regensburg Institut für Analytische Chemie, Chemo- und Biosensorik 93040 Regensburg

More information

Data-intensive HPC: opportunities and challenges. Patrick Valduriez

Data-intensive HPC: opportunities and challenges. Patrick Valduriez Data-intensive HPC: opportunities and challenges Patrick Valduriez Big Data Landscape Multi-$billion market! Big data = Hadoop = MapReduce? No one-size-fits-all solution: SQL, NoSQL, MapReduce, No standard,

More information

Aaron Ponti. Single Cell Unit, D-BSSE ETHZ (Basel) aaron.ponti@bsse.ethz.c h

Aaron Ponti. Single Cell Unit, D-BSSE ETHZ (Basel) aaron.ponti@bsse.ethz.c h Aaron Ponti Single Cell Unit, D-BSSE ETHZ (Basel) aaron.ponti@bsse.ethz.c h Raw data annotated backed up centralized storage HRM 2 openbis open Biology Information System openbis is an extensible, open

More information

Katharina Lückerath (AG Dr. Martin Zörnig) adapted from Dr. Jörg Hildmann BD Biosciences,Customer Service

Katharina Lückerath (AG Dr. Martin Zörnig) adapted from Dr. Jörg Hildmann BD Biosciences,Customer Service Introduction into Flow Cytometry Katharina Lückerath (AG Dr. Martin Zörnig) adapted from Dr. Jörg Hildmann BD Biosciences,Customer Service How does a FACS look like? FACSCalibur FACScan What is Flow Cytometry?

More information

Chapter 10 Immunofluorescence

Chapter 10 Immunofluorescence Chapter 10 Immunofluorescence J. Paul Robinson PhD, Jennifer Sturgis BS and George L. Kumar PhD Immunofluorescence (IF) is a common laboratory technique used in almost all aspects of biology. This technique

More information

CHAPTER 3 OBSERVING MICROORGANISMS THROUGH A MICROSCOPE. I. UNITS OF MEASUREMENT - See Table 3.1 in text. + Fig. 3.2

CHAPTER 3 OBSERVING MICROORGANISMS THROUGH A MICROSCOPE. I. UNITS OF MEASUREMENT - See Table 3.1 in text. + Fig. 3.2 CHAPTER 3 OBSERVING MICROORGANISMS THROUGH A MICROSCOPE I. UNITS OF MEASUREMENT - See Table 3.1 in text. + Fig. 3.2 II. MICROSCOPY: THE INSTRUMENTS A. COMPOUND LIGHT MICROSCOPY Figure 3.3 1. Have ocular

More information

LABORATORY 2 THE CELL CYCLE AND THE STAGES OF MITOSIS LEARNING OBJECTIVES AFTER COMPLETING THIS LABORATORY, YOU SHOULD BE ABLE TO:

LABORATORY 2 THE CELL CYCLE AND THE STAGES OF MITOSIS LEARNING OBJECTIVES AFTER COMPLETING THIS LABORATORY, YOU SHOULD BE ABLE TO: LABORATORY 2 THE CELL CYCLE AND THE STAGES OF MITOSIS LEARNING OBJECTIVES AFTER COMPLETING THIS LABORATORY, YOU SHOULD BE ABLE TO: 1. Describe the cell cycle. 2. Identify stages of mitosis from prepared

More information

Laboratory Observing the Cell Cycle of Onion Root Tip Cells

Laboratory Observing the Cell Cycle of Onion Root Tip Cells Laboratory Observing the Cell Cycle of Onion Root Tip Cells Background: Because of their rapid growth, the cells of the root tips of plants undergo rapid cell division. Ornamental onion root tips cells

More information

SOFTWARE FOR 3D IMAGE VISUALISATION, ANALYSIS AND MODEL GENERATION

SOFTWARE FOR 3D IMAGE VISUALISATION, ANALYSIS AND MODEL GENERATION SOFTWARE FOR 3D IMAGE VISUALISATION, ANALYSIS AND MODEL GENERATION Solutions for Life Sciences SIMPLEWARE SOFTWARE Simpleware provides easy-to-use software solutions for the processing of 3D image data

More information

Data. microcat +SPECT

Data. microcat +SPECT Data microcat +SPECT microcat at a Glance Designed to meet the throughput, resolution and image quality requirements of academic and pharmaceutical research, the Siemens microcat sets the standard for

More information

Archival and Retrieval in Digital Pathology Systems

Archival and Retrieval in Digital Pathology Systems Archival and Retrieval in Digital Pathology Systems Authors: Elizabeth Chlipala (Premier Laboratories), Jesus Elin (Yuma Regional Medical Center), Ole Eichhorn (Aperio Technologies), Malini Krishnamurti

More information

IMARIS. 3D and 4D interactive analysis and visualization solutions for the life sciences.

IMARIS. 3D and 4D interactive analysis and visualization solutions for the life sciences. IMARIS 3D and 4D interactive analysis and visualization solutions for the life sciences. IMARIS A Brief History For over 20 years Bitplane has offered enabling scientific software tools for the life science

More information

FDA Regulation of Whole Slide Imaging (WSI) Devices: Current Thoughts

FDA Regulation of Whole Slide Imaging (WSI) Devices: Current Thoughts FDA Regulation of Whole Slide Imaging (WSI) Devices: Current Thoughts Clinical Laboratory Improvement Advisory Committee Meeting Centers for Disease Control and Prevention February 15, 2012 Tremel A. Faison,

More information

Zeiss Axioimager M2 microscope for stereoscopic analysis.

Zeiss Axioimager M2 microscope for stereoscopic analysis. Zeiss Axioimager M2 microscope for stereoscopic analysis. This system is fully motorized and configured with bright field and multi-channel fluorescent. It works with Stereo Investigator, Neurolucida,

More information

Creative Director. Inspire artists, programmers, producers and marketing staff to make the highest quality product possible

Creative Director. Inspire artists, programmers, producers and marketing staff to make the highest quality product possible Open positions Creative Director... 2 Level designer... 3 Data scientist... 4 Backend engineer - user acquisition and game management tools... 5 Gameplay programmer... 6 Software engineer Client, tools,

More information

MiSeq: Imaging and Base Calling

MiSeq: Imaging and Base Calling MiSeq: Imaging and Page Welcome Navigation Presenter Introduction MiSeq Sequencing Workflow Narration Welcome to MiSeq: Imaging and. This course takes 35 minutes to complete. Click Next to continue. Please

More information

Pathology Images, DICOM, and LIS/PACS Integration. Harry Solomon, GE Healthcare Co-Chair, DICOM WG-20 / HL7 Imaging Integration WG

Pathology Images, DICOM, and LIS/PACS Integration. Harry Solomon, GE Healthcare Co-Chair, DICOM WG-20 / HL7 Imaging Integration WG Pathology Images, DICOM, and LIS/PACS Integration, GE Healthcare Co-Chair, DICOM WG-20 / HL7 Imaging Integration WG Disclosure Employee, GE Healthcare 2 Pathology Informatics 2012 Topics Brief overview

More information

Version 8 DICOM Conformance Statement. Version 3.04, September 2014

Version 8 DICOM Conformance Statement. Version 3.04, September 2014 Version 8 DICOM Conformance Statement Version 3.04, September 2014 1 Conformance Statement Overview The application described in this Conformance Statement VEPRO EMR Manager PACS is a collection of processes

More information

Supports screening, diagnostic, and multimodality workflows

Supports screening, diagnostic, and multimodality workflows GE Healthcare Universal Viewer Breast Imaging Product Data Sheet Supports screening, diagnostic, and multimodality workflows Introduction Centricity PACS with Universal Viewer 1 puts clinical insight within

More information

FluorChem Q. A Quantitative Western Blot Imaging Solution

FluorChem Q. A Quantitative Western Blot Imaging Solution FluorChem Q A Quantitative Western Blot Imaging Solution Contents FluorChem Q Innovative Design The FluorChem Q is a total solution for quantitative fluorescent and chemiluminescent Western blot imaging

More information

Zeiss Laser Scanning Microscope 510. Zuidhorst 178. For more information contact. Tom Groothuis. ZH153, t.a.m.groothuis@utwente.nl

Zeiss Laser Scanning Microscope 510. Zuidhorst 178. For more information contact. Tom Groothuis. ZH153, t.a.m.groothuis@utwente.nl Zeiss Laser Scanning Microscope 510 Zuidhorst 178 For more information contact Tom Groothuis ZH153, t.a.m.groothuis@utwente.nl Start Hardware Remove the blue dust cap from the microscope. If needed, turn

More information

Basics of Image and data analysis in 3D

Basics of Image and data analysis in 3D Basics of Image and data analysis in 3D outline Why image processing, and how? Image processing in 2D What is an ideal image? Histogram tells stories! Before taking the image: the right imaging conditions!

More information

3D Building Roof Extraction From LiDAR Data

3D Building Roof Extraction From LiDAR Data 3D Building Roof Extraction From LiDAR Data Amit A. Kokje Susan Jones NSG- NZ Outline LiDAR: Basics LiDAR Feature Extraction (Features and Limitations) LiDAR Roof extraction (Workflow, parameters, results)

More information

CERTIFIED MULESOFT DEVELOPER EXAM. Preparation Guide

CERTIFIED MULESOFT DEVELOPER EXAM. Preparation Guide CERTIFIED MULESOFT DEVELOPER EXAM Preparation Guide v. November, 2014 2 TABLE OF CONTENTS Table of Contents... 3 Preparation Guide Overview... 5 Guide Purpose... 5 General Preparation Recommendations...

More information

Recording the Instrument Response Function of a Multiphoton FLIM System

Recording the Instrument Response Function of a Multiphoton FLIM System Recording the Instrument Response Function of a Multiphoton FLIM System Abstract. FLIM data analysis in presence of SHG signals or extremely fast decay components requires the correct instrument response

More information

Archival and Retrieval in Digital Pathology Systems

Archival and Retrieval in Digital Pathology Systems Archival and Retrieval in Digital Pathology Systems Authors: Elizabeth Chlipala (Premier Laboratory), Jesus Elin (Yuma Regional Medical Center), Ole Eichhorn (Aperio Technologies), André Huisman (University

More information

IBM's Fraud and Abuse, Analytics and Management Solution

IBM's Fraud and Abuse, Analytics and Management Solution Government Efficiency through Innovative Reform IBM's Fraud and Abuse, Analytics and Management Solution Service Definition Copyright IBM Corporation 2014 Table of Contents Overview... 1 Major differentiators...

More information

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification Gold Standard for Quantitative Data Processing Because of the sensitivity, selectivity, speed and throughput at which MRM assays can

More information

Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments

Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments Mario Cannataro, Pietro Hiram Guzzi, Tommaso Mazza, and Pierangelo Veltri University Magna Græcia of Catanzaro, 88100

More information

AxioCam HR The Camera that Challenges your Microscope

AxioCam HR The Camera that Challenges your Microscope Microscopy from Carl Zeiss AxioCam HR The Camera that Challenges your Microscope Documentation at the edge of the visible The Camera for Maximum Success: AxioCam HR Low light fluorescence, live cell imaging,

More information

Measuring Cell Viability/Cytotoxicity: Cell Counting Kit-F

Measuring Cell Viability/Cytotoxicity: Cell Counting Kit-F Introduction The Cell Counting Kit-F is a fluorometic assay for the determination of viable cell numbers. Calcein-AM in this kit passes through the cell membrane and is hydrolized by the esterase in the

More information

Medflow Imaging DICOM Server

Medflow Imaging DICOM Server DICOM Server version 7.6.2 Revision 2.0 Copyright 2011 Medflow, Inc. Revision History Date June 14, 2011 August 30, 2011 Rev Description 7.6.1 First version. 7.6.2 Revised to reflect version 7.6.2 changes

More information

CLINICAL information systems (CIS) have developed

CLINICAL information systems (CIS) have developed IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, VOL. 11, NO. 2, MARCH 2007 127 Addressing the Future of Clinical Information Systems Web-Based Multilayer Visualization Chueh-Loo Poh, Richard

More information

Webex-based remote instrument control guide

Webex-based remote instrument control guide Webex-based remote instrument control guide 1) Once a microscopic imaging experiment is scheduled, the host (i.e., Hunter Bioimaging Facility) will send an email containing a Webex meeting link to the

More information

Interoperability between Anatomic Pathology Laboratory Information Systems and Digital Pathology Systems

Interoperability between Anatomic Pathology Laboratory Information Systems and Digital Pathology Systems Interoperability between Anatomic Pathology Laboratory Information Systems and Digital Pathology Systems Authors: Jesus Ellin (Yuma Regional Medical Center), Anna Haskvitz (Sunquest Information Systems,

More information