Using Virtual Slides in Medical Education Using Virtual Slides in Medical Education with the Virtual Slice Systemwith the Virtual Slice System

Jack Glaser, President Jack Glaser, President MicroBrightField, Inc.MicroBrightField, Inc.

Advantages of Virtual Slides Advantages of Virtual Slides Overview

0.08x

Single section 0.63x

Anatomic detail 5x

Cellular detail20x

Multiple levels of resolution are available from a virtual slide

Entire 2”x3” inch slide scanned Entire 2”x3” inch slide scanned with a 20x objective (~300x with a 20x objective (~300x absolute absolute magmag). It is not ). It is not possible to see this large a possible to see this large a fieldfield--ofof--view with a standard view with a standard microscope.microscope. Even a single section overviewEven a single section overview

is impossible with a microscopeis impossible with a microscope

Key instructional benefitsKey instructional benefitsThe images are of highest quality and represent all The images are of highest quality and represent all modalities of optical microscopymodalities of optical microscopyImage collections can be updated as new material Image collections can be updated as new material becomes availablebecomes availableImages can be shared with other institutionsImages can be shared with other institutionsMaterial can be used for both instruction and testingMaterial can be used for both instruction and testingSlides can be accessed from outside traditional lab Slides can be accessed from outside traditional lab timestimes

Key Economic BenefitsKey Economic Benefits

Reduces or eliminates the need for Reduces or eliminates the need for microscopesmicroscopesNo more replacing lost or broken slidesNo more replacing lost or broken slidesReduces need for lab spaceReduces need for lab space

Viewer

Virtual Slide Technology ComponentsVirtual Slide Technology Components

Virtual Slide Acquisition Virtual Slide Acquisition MethodsMethods

1.1. Montage ScanningMontage ScanningCan be used with existing microscopesCan be used with existing microscopesCan obtain images from other forms of Can obtain images from other forms of microscopy, i.e. fluorescencemicroscopy, i.e. fluorescenceMore EconomicalMore Economical

2.2. Strip ScanningStrip ScanningFast Scan SpeedFast Scan Speed

Montage ScanningMontage Scanning

Motorized stage and digital camera used to Motorized stage and digital camera used to acquire an image at each fieldacquire an image at each field--ofof--viewview

MBF Scanning TechnologyMBF Scanning TechnologyAcquisition with Virtual Slice technologyAcquisition with Virtual Slice technology

Acquisition with standard research microscopeAcquisition with standard research microscope

Video or digital Video or digital cameracamera

Motorized stageMotorized stageand stageand stagecontroller controller

Microscope with Microscope with high quality opticshigh quality optics

Computer with Computer with MicroBrightField MicroBrightField software and software and video capture video capture cardcard

MBF Scanning TechnologyMBF Scanning Technology

Acquisition with Virtual Slice technologyAcquisition with Virtual Slice technologyMany illumination techniques can be usedMany illumination techniques can be used

Brightfield, darkfield, fluorescence, etc.Brightfield, darkfield, fluorescence, etc.

Fluorescently stained (GFP) Fluorescently stained (GFP) mouse brain acquired at 40xmouse brain acquired at 40x

MBF Scanning TechnologyMBF Scanning Technology

Acquisition with Virtual Slice technologyAcquisition with Virtual Slice technologyMany slide formats can be usedMany slide formats can be used

Such as 1”x3” slides, 2”x3” Such as 1”x3” slides, 2”x3” slides, large format slides, slides, large format slides, even an entire section of a even an entire section of a human headhuman head

Virtual Slide TechnologyVirtual Slide TechnologyAcquisition with Virtual Slice technologyAcquisition with Virtual Slice technology

Acquisition with standard research microscopeAcquisition with standard research microscopeEach fieldEach field--ofof--view acquired in sequence, seamlessly stitched to view acquired in sequence, seamlessly stitched to adjacent fields. Amount of blending and matching controlled by adjacent fields. Amount of blending and matching controlled by the the user user Extremely large image files are generatedExtremely large image files are generated

Typical:Typical:Digital acquisition of 40 x 40 fields of view with 40x objectiveDigital acquisition of 40 x 40 fields of view with 40x objective

(~7 x 7 mm piece of tissue)(~7 x 7 mm piece of tissue)Each field is 4MB, total uncompressed image size ~6.5GBEach field is 4MB, total uncompressed image size ~6.5GB

Challenging:Challenging:Acquisition of entire human cerebellum with 20x objectiveAcquisition of entire human cerebellum with 20x objectiveUncompressed size: 97.5 GBUncompressed size: 97.5 GB

How to view, manage, and distribute such large files?How to view, manage, and distribute such large files?

Using an Effective Virtual Slide ViewerUsing an Effective Virtual Slide Viewer

An effective virtual slide viewer has the following attributes:An effective virtual slide viewer has the following attributes:

The virtual slide may be viewed at any magnification, up The virtual slide may be viewed at any magnification, up to the magnification of acquisitionto the magnification of acquisitionThe virtual slide may be dynamically explored in any The virtual slide may be dynamically explored in any region at any magnificationregion at any magnificationMultiple people can view a slide simultaneouslyMultiple people can view a slide simultaneouslyThe functionality is familiar to users of traditional The functionality is familiar to users of traditional microscopesmicroscopesVirtual slides stored in various file formats can be Virtual slides stored in various file formats can be seamlessly viewedseamlessly viewed

Virtual Slide Storage FormatsVirtual Slide Storage Formats

Virtual slides can be stored as a single large Virtual slides can be stored as a single large file or as a multitude of smaller filesfile or as a multitude of smaller files

Advantages of a Single Large FileAdvantages of a Single Large FileCan use industry standard file formatsCan use industry standard file formatsLess complex to manageLess complex to manage

Advantages of Multitude of FilesAdvantages of Multitude of Files??

File Formats for Virtual SlidesFile Formats for Virtual SlidesProblemProblem Large storage requirements Large storage requirements

SolutionSolution Use Proven Image Compression Use Proven Image Compression TechniquesTechniques

FlashpixFlashpix format (JPEG)format (JPEG)ZoomifyZoomify (JPEG)(JPEG)MrSIDMrSID (Wavelet)(Wavelet)JPEG2000 (Wavelet)JPEG2000 (Wavelet)

Note: many popular formats have size limitationsNote: many popular formats have size limitationsi.e. the limitation of TIFF format is 2GBi.e. the limitation of TIFF format is 2GB

File Formats for Virtual SlidesFile Formats for Virtual SlidesCompression Formats Compression Formats ---- WaveletWavelet vs. JPEG vs. JPEG

Wavelet compression allows for greater compression Wavelet compression allows for greater compression at greater computational expense (slower to create, at greater computational expense (slower to create, slower to view)slower to view)

Typical Wavelet Compression: 6.5GB Typical Wavelet Compression: 6.5GB →→125MB125MB

JPEG compression is faster and less computationally JPEG compression is faster and less computationally intenseintense

Typical JPEG Compression: 6.5GBTypical JPEG Compression: 6.5GB→→550MB550MB

File Formats for Virtual SlidesFile Formats for Virtual SlidesIs a proprietary file format a potential Is a proprietary file format a potential problem?problem?

pro·pri·e·tarypro·pri·e·tary11 :: one that possesses, owns, or holds exclusive right to somethingone that possesses, owns, or holds exclusive right to something; ; specificallyspecifically22 :: something that is used, produced, or marketed under exclusive lsomething that is used, produced, or marketed under exclusive legal egal right of the inventor or maker; right of the inventor or maker; specificallyspecifically :: a drug (as a patent medicine) a drug (as a patent medicine) that is protected by secrecy, patent, or copyright against free that is protected by secrecy, patent, or copyright against free competition competition as to name, product, composition, or process of manufacture as to name, product, composition, or process of manufacture

Merriam WebsterMerriam Webster

Nearly every image file format, i.e., TIFF, BMP, GIF, etc. is byNearly every image file format, i.e., TIFF, BMP, GIF, etc. is by definition #1definition #1Files in category #2 might be a problemFiles in category #2 might be a problem

Viewing Virtual SlidesViewing Virtual SlidesProblem:Problem:

Large files are sluggish to load in image Large files are sluggish to load in image programs such as Photoshop, Corel, etc.programs such as Photoshop, Corel, etc.

A 1GB file typically takes >5 minutes to loadA 1GB file typically takes >5 minutes to load

Solution:Solution:We developed an innovative webWe developed an innovative web--based viewer based viewer

Only the requested fieldOnly the requested field--ofof--view is transmittedview is transmittedFast, dynamic viewing of slidesFast, dynamic viewing of slides

File Formats for Virtual SlidesFile Formats for Virtual SlidesProblem Problem Retrieving select data from a large Retrieving select data from a large

traditional image file is time consumingtraditional image file is time consumingSolutionSolution Images are stored in a multiImages are stored in a multi--resolution resolution

pyramidal formatpyramidal formatA multiA multi--resolution file format allows images to be stored at different rresolution file format allows images to be stored at different resolutions for different esolutions for different purposes. Each resolution is divided into 64 x 64 blocks. Withinpurposes. Each resolution is divided into 64 x 64 blocks. Within a block, pixels can be either a block, pixels can be either uncompressed, JPEG compressed or singleuncompressed, JPEG compressed or single--color compressed. Image is color compressed. Image is downsampleddownsampledduring storage allowing for fastest visibility.during storage allowing for fastest visibility.

Virtual Slide ViewerVirtual Slide ViewerStandard Standard BrowserBrowserWindowWindow

Slide AreaSlide Area

Text Text Information Information about Slideabout Slide Panning ToolPanning Tool

Thumbnail Thumbnail of Entire of Entire SlideSlide

Magnification Magnification controlcontrol

Zoom ToolsZoom Tools

Current ViewCurrent View

Virtual Slide ViewerVirtual Slide ViewerViewer is a Java applet, works on multiple platforms Viewer is a Java applet, works on multiple platforms

without need to download plugwithout need to download plug--insinsWindows Explorer 5.0 and higherWindows Explorer 5.0 and higherMacOSMacOS 10.2 and higher10.2 and higherLinuxLinuxSolarisSolaris

Easily viewed on a typical desktop computerEasily viewed on a typical desktop computer128 MB RAM128 MB RAM500 MHz processor500 MHz processorWin98 or laterWin98 or later

The images reside on a server computerThe images reside on a server computer

Internet Virtual Slide ViewerInternet Virtual Slide ViewerServer sends only the selected fieldServer sends only the selected field--ofof--view view

Made up of many 64x64 fields (~1KB each)Made up of many 64x64 fields (~1KB each)

Close up of macro view Close up of macro view shows extensive shows extensive compression within a compression within a single blocksingle block

When a small, high magnification fieldWhen a small, high magnification field--ofof--view is view is requested, a group of blocks from a more detailed requested, a group of blocks from a more detailed level of the pyramid are sent.level of the pyramid are sent.

~5µm/pixel, 1 block~5µm/pixel, 1 block

~0.16µm/pixel, ~0.16µm/pixel, Many blocksMany blocks

Many blocksMany blocks

Internet Virtual Slide ViewerInternet Virtual Slide Viewer

This slide view shows completed blocks as they load.This slide view shows completed blocks as they load.Previously viewed blocks are cached for repeat viewingPreviously viewed blocks are cached for repeat viewing

Internet Virtual Slide ViewerInternet Virtual Slide Viewer

Example: Viewing a virtual slide of a human jawExample: Viewing a virtual slide of a human jaw(Next Generation of the Visible Human feasibility study)(Next Generation of the Visible Human feasibility study)

Virtual Slide Virtual Slide ViewerViewer

University of Iowa medical histology instructionUniversity of Iowa medical histology instruction

Our Java viewer applet is Our Java viewer applet is easy to insert into custom easy to insert into custom Web pages for maximum Web pages for maximum

flexibility flexibility JSP, ASP, PHP, etc.

CSULB Avian brain atlas creationCSULB Avian brain atlas creation

JSP, ASP, PHP, etc. Ohio State University tissue Ohio State University tissue microarraymicroarray visualizationvisualization

Internet Slide ViewerInternet Slide Viewer

What kind of Internet connection is What kind of Internet connection is required? required?

Typical download times for a single fieldTypical download times for a single field--ofof--view:view:

LANLAN 0.9 seconds0.9 secondsT1T1 1.5 seconds1.5 secondsDSL/CableDSL/Cable 4 seconds4 secondsDialDial--up Modemup Modem 1 minute1 minute

Enhancements with Virtual Slide ViewingEnhancements with Virtual Slide Viewing

In addition to viewing at multiple magnifications, the virtual In addition to viewing at multiple magnifications, the virtual slide platform allows for many enhancements to the slide platform allows for many enhancements to the microscopic slide material:microscopic slide material:

Store locations on a slideStore locations on a slideCreate graphical overlaysCreate graphical overlaysStore overlays with specific locationsStore overlays with specific locationsStore text descriptions of the slide or a specific Store text descriptions of the slide or a specific location on the slidelocation on the slideCreate hyperlink labelsCreate hyperlink labelsPerform quantitative measurements of slide Perform quantitative measurements of slide materialmaterial

Virtual Slide ViewerVirtual Slide Viewer

Macro View, Macro View, Pan and Zoom Pan and Zoom toolstools

Simplified viewer window provides Simplified viewer window provides easy access to navigation tools easy access to navigation tools and slide information

Text information about the Text information about the slide, hyperlinks, and links slide, hyperlinks, and links to specific viewsto specific views and slide information

Virtual Slide ViewerVirtual Slide Viewer

Labeling toolsLabeling tools

The labeling window provides easy access to the labeling tools. The labeling window provides easy access to the labeling tools. Labeling Labeling tools allow for the nontools allow for the non--destructive addition of arrows, text, contours, destructive addition of arrows, text, contours, measurements, etc., to the slide view. Labels can be attached tmeasurements, etc., to the slide view. Labels can be attached to all views o all views or to limited magnifications.or to limited magnifications.

Virtual Slide ViewerVirtual Slide ViewerCustomizable Labeling toolsCustomizable Labeling tools

Types of LabelsTypes of Labels••TextText••ArrowsArrows••Text and Text and

ArrowsArrows••MonocleMonocle••ContoursContours

••Full range of ColorsFull range of Colors••Customizable FontsCustomizable Fonts••Link to any MagnificationLink to any Magnification••Analysis of contour sizesAnalysis of contour sizes

Virtual Slide ViewerVirtual Slide Viewer

ProblemProblemUsing traditional labeling techniques Using traditional labeling techniques

makes labels appropriate for one level of makes labels appropriate for one level of zoom onlyzoom only

SolutionSolutionLabels stored separately from image Labels stored separately from image

files in vector formatfiles in vector format

Virtual Slide ViewerVirtual Slide ViewerLabels added in separate layer from the imageLabels added in separate layer from the image

Labels shown Labels shown appropriately sized appropriately sized for viewing when for viewing when labels are stored in labels are stored in an independent an independent layerlayer

If label is part If label is part of the image, of the image, zooming in zooming in makes text makes text inappropriately inappropriately largelarge

Virtual Slide TechnologyVirtual Slide TechnologyProblemProblem

How to store and manage large numbers How to store and manage large numbers of virtual slides?of virtual slides?

SolutionSolutionDevelopment of interoperable slide Development of interoperable slide management system (database)management system (database)

Virtual Slide ManagementVirtual Slide ManagementDatabase StorageDatabase Storage

Database enables simple querying of image contents, Database enables simple querying of image contents, e.g., species, organ, slide preparation, etc.e.g., species, organ, slide preparation, etc.Collection of virtual slides stored with related Collection of virtual slides stored with related information, slide labels, text notes. information, slide labels, text notes. Create class content and quizzes Create class content and quizzes Maintain all information about the slidesMaintain all information about the slidesInteroperability (via a federation model) allows the Interoperability (via a federation model) allows the ability to find slides in other databases when ability to find slides in other databases when databases are linkeddatabases are linked

Virtual Slide ManagementVirtual Slide ManagementDatabase StorageDatabase Storage

What are the demands of the server?What are the demands of the server?Minimum Hardware:Minimum Hardware:

1 GHz Processor1 GHz Processor1 GB RAM1 GB RAMWindows 2000, Linux, Solaris OSWindows 2000, Linux, Solaris OS

Architecture is scalable, allowing for division Architecture is scalable, allowing for division onto multiple machines, web server and onto multiple machines, web server and image serverimage server

Virtual Slide ManagementVirtual Slide Management

ProblemProblemMany students need to access the slides at one Many students need to access the slides at one timetime

SolutionSolutionLoad balancing servers automatically distribute Load balancing servers automatically distribute the computational demands to other computersthe computational demands to other computers

Virtual Slide ManagementVirtual Slide ManagementServer Load BalancingServer Load Balancing

One server 30 simultaneous usersOne server 30 simultaneous users

With Virtual Slice load balancing capabilityWith Virtual Slice load balancing capabilityservers can handle unlimited users servers can handle unlimited users

Examples of Integration of Viewer Examples of Integration of Viewer and Databaseand DatabaseComposing a QuizComposing a Quiz

Instructor finds area on slide, outlines region, types in questiInstructor finds area on slide, outlines region, types in question and on and answer. All information is maintained in the database.answer. All information is maintained in the database.

Examples of Integration of Viewer Examples of Integration of Viewer and Databaseand Database

Taking a QuizTaking a Quiz

Student later is automatically taken to the area on the slide, aStudent later is automatically taken to the area on the slide, and nd sees the question. The student may enter her answer.sees the question. The student may enter her answer.

Examples of Integration of Viewer Examples of Integration of Viewer and Databaseand Database

Self QuizzingSelf Quizzing

The student may test their knowledge on their own. The student The student may test their knowledge on their own. The student sees the answer after clicking on the Show Answer button.sees the answer after clicking on the Show Answer button.

Examples of Integration of Viewer Examples of Integration of Viewer and Databaseand Database

Side by Side Slide ComparisonSide by Side Slide Comparison

Color Balancing and Color Balancing and ModificationModification

White balance and color adjustments may be madeWhite balance and color adjustments may be made

Alternative Virtual Slide Storage Alternative Virtual Slide Storage TechnologyTechnology

Virtual Slide StorageVirtual Slide StorageVirtual slides and viewer can also be set up Virtual slides and viewer can also be set up on a single machine, or distributed on a CD.on a single machine, or distributed on a CD.

Limitations: Limitations: Number of slides limited by hard drive space or CD Number of slides limited by hard drive space or CD spacespaceNo interactivityNo interactivityDifficult to updateDifficult to update

Advantages:Advantages:No network neededNo network neededConvenient where highConvenient where high--speed Internet is not availablespeed Internet is not available

How does a professor use a How does a professor use a virtual slide?virtual slide?

Selects the slides to Selects the slides to be used in the be used in the class.class.Edits and revises Edits and revises the slides to insert the slides to insert markers, markers, annotations, annotations, comments, and comments, and questions.questions.Links the slides to Links the slides to other didactic other didactic material to create a material to create a unified course unified course presentation.presentation.

How does a student use the How does a student use the virtual slide?virtual slide?

Logs in to the web site or local server from their Logs in to the web site or local server from their computercomputerSelects the course material or the slides of interestSelects the course material or the slides of interestNavigates through the slide at his/her discretion, Navigates through the slide at his/her discretion, observing the morphology, noting comments, observing the morphology, noting comments, answering questionsanswering questionsAsks questions to teacherAsks questions to teacherLogs offLogs off

The Future of Virtual SlidesThe Future of Virtual SlidesIncrease in image quality, automation, and Increase in image quality, automation, and acquisition speedacquisition speed

Creation of 3D virtual slides (multiple focal planes)Creation of 3D virtual slides (multiple focal planes)

Increase in content quality available on webIncrease in content quality available on webArchived collections of pathological specimensArchived collections of pathological specimensArchived collections of research specimensArchived collections of research specimens

Widespread use of virtual slides in clinical useWidespread use of virtual slides in clinical use

ConclusionConclusionVirtual slide technology is a rapidly emerging Virtual slide technology is a rapidly emerging field enabling unprecedented availability for field enabling unprecedented availability for accessing microscopic specimensaccessing microscopic specimens

Virtual slide viewers enhance the functionality of Virtual slide viewers enhance the functionality of microscope with ability to store locations, add microscope with ability to store locations, add annotations, link to other sites and information.annotations, link to other sites and information.

In many situations, virtual slides have distinct In many situations, virtual slides have distinct advantages over traditional glass slides.advantages over traditional glass slides.

Current technology makes the use of virtual Current technology makes the use of virtual