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Acquisition and Use of Digital Images for Pathology Education and Practice APIII 2002 Peter G. Anderson, DVM, PhD Kristo PowerPoint Presentation
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Acquisition and Use of Digital Images for Pathology Education and Practice APIII 2002 Peter G. Anderson, DVM, PhD Kristopher Jones, MD-MPH Candidate Department of Pathology University of Alabama at Birmingham. Co-conspirators. University of Alabama at Birmingham

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Acquisition and Use of Digital Images for Pathology Education and Practice

APIII 2002

Peter G. Anderson, DVM, PhD

Kristopher Jones, MD-MPH Candidate

Department of Pathology

University of Alabama at Birmingham

co conspirators

University of Alabama at Birmingham

Department of Pathology

  • Sate Hamza, M.D.
  • J. Alan Long, M.D.
  • Kristina T. C. Panizzi, M.A.E.

Pathology Education Instructional Resource

  • Focus on the basics of using digital images in pathology education and practice
    • Acquisition
    • Processing and Editing
    • Storage
    • Management
    • Delivery
  • Focus on Web-based delivery of images through Perl-centered imaging solutions
  • Other resources at APIII 2002
    • Boot Camp
    • Breakout Sessions
      • Dr. Harrison & Dr. Berman’s “Programming for Pathology Informatics: Why Should I Learn to Program?”
      • Ms. Yagi & Dr. Gilbertson’s “Practical Telepathology: Applications and Implementation Issues”
      • Dr. Berman’s “Programming for Pathology Informatics: Perl Programming Tutorial - Tools for Pathology Informatics”
    • E-Posters/Scientific Sessions
    • Exhibitors
  • Online resources—
  • What we do/know best (or so we think)
    • Acquisition of large numbers of still digital images
      • Using film scanners, flatbed scanners, digital capture from analog sources, conversion of existing digital materials, and de novo digital acquisition
    • Automated processing/editing of images
    • Storage/management of image collections
    • Web-based delivery of image collections
  • Secondary issues
    • Efficient solutions (automation, where possible)
    • Low-cost solutions
    • Non-proprietary solutions
    • Perl-based solutions
why me why now
Why me? Why now?
  • Images “R” Us
    • Pathology is image-intensive and imaging is rapidly becoming (or “has become” to many) a digital discipline
      • This is our fourth year at APIII and we have seen the transformation first-hand
  • In a well-implemented digital imaging system, efficiency is maximized
  • Costs are falling
    • Considering all the costs, “going digital” can be cheaper
  • Allows rapid repurposing of resources, which can help raise the dead from the…
the image graveyard
TheImage Graveyard
  • Most pathologists have thousands of slides usually lying dormant and collecting dust
  • “But I have the latest 6-megapixel FireWire-enabled digital camera!”
    • Doesn’t matter what you use if you don’t know how to use it
    • You just create a digital image graveyard (with fresh additions being added daily)
    • Image acquisition is actually the easiest, most straightforward part of the process of “going digital”
  • Issues (“I thought you said this was easy!”)
    • Subject matter and media
      • Gross vs. microscopic
      • de novo capture vs. film vs. print vs. glass slide etc.
    • Output requirements
      • Monitor vs. print vs. film recorder
    • File size limitations
      • Method of delivery—file media vs. network
      • Storage considerations
      • Volume
    • Hardware/software capabilities, limitations, costs
  • Making it easy: GIGO(Garbage In, Garbage Out)
    • Most issues of acquisition can be solved by asking “What’s the most demanding need I will ever have of this image?” and then acquiring the image in a way that meets that need
    • As said previously, acquisition is the easy part
      • Capturing/scanning a digital image takes seconds
      • Processing, editing, converting, categorizing, organizing, and archiving is where the real time expenditure occurs
      • All that time is wasted, however, if the size/quality of the original capture doesn’t meet your final needs
  • So, the real issue is resolution
    • All the other issues are secondary to the real concern of “how big an image do I need?”
    • Once you know that crucial piece of information, the specifications for hardware, software, storage needs, costs, etc. become obvious
      • If you NEED a 750 Mb digital image file then you NEED something that will capture an image of that size and hardware/media on which to store it and your other 750 Mb scans

  • How big an image do I need?
    • Print demands are usually the largest, so that’s a logical measure to use
    • 300 ppi (~dpi) is sufficient for most print applications
print resolution
Print Resolution
  • Formula for determining necessary resolution for print:

(Print width (in.) x 300 ppi) x (Print height (in.) x 300 ppi)

    • If you need to print out an 8”x12” image, then you need to acquire the image at 2400x3600 pixels
    • If the original media is a 1”x1.5” 35mm slide, then you need a scanner capable of producing 2400 ppi (2400/1; 3600/1.5) to produce a final image of sufficient quality
    • This image file would be approximately 25Mb in size in uncompressed (lossless) TIFF format
  • Meet your largest need
    • While you may not need a 25Mb version for most applications, if you envision you may need it at some point it may be worth your while to acquire it the first time
    • By the time you crop, color correct, sharpen, rubber stamp, and level your image you’ll be glad you don’t have to do it again
  • Do I really need a 25Mb file?
    • Probably not
    • We have found that for most of our needs, being able to print out a 3.33”x5” image is sufficient
      • Pathology Reports
      • Journal publication
    • Using our formula, we need a 1000x1500 pixel image
      • Our scanner must provide 1000 ppi capability
      • The resulting file is ~4.5 Mb in size
      • At native size (1”x1.5”) we can print out the image to a film recorder at the original resolution of 1000 ppi
    • An image of this size meets the needs of almost any electronic delivery medium
      • Except for virtual microscopy (case example of PEIR Digital Library)
  • What kind of hardware do I need to capture images of this size?
    • Analog Video Camera with Capture Card
    • Digital Camera
    • Film Camera and Scanner
      • Film
      • Flatbed
      • Drum
  • Analog Cameras with Capture Card
    • Digital image generated by analog to digital converting capture card installed on computer
    • Advantages
      • Capture cards are cheap if you already have the analog camera
      • Good for video (real-time)
    • Disadvantages
      • Low resolution VGA quality (640x480 only, but interpolation possible)
      • Low quality of analog video signal
  • Digital Cameras
    • Analog voltages are converted at camera to produce digital output
    • Rapidly evolving technology with new models, new features, and lower prices being offered every day
    • Various grades depending on technology, number of pixels, size of pixels, connection interface, and real-time capabilities
    • Even the consumer-grade cameras, however, can sufficiently meet most needs
  • Digital Cameras
    • For our purposes today, in answering the question “what am I going to do with this image?”, the matter comes down to megapixels
    • How many megapixels do I need?
      • High-end prosumer cameras support 5-6 megapixels, do you really need to splurge on one (though prices are dropping fast)?
      • Perhaps, if you need to print an 8”x10” image at 240 dpi (1920x2560)
      • However, a much less pricey 3 megapixel camera will easily print a 5”x7” image at 300 dpi
  • Film scanners
    • Technology
      • Transmits light through the image rather than reflecting it off the image as do flatbed scanners
    • Advantages
      • Capture existing film resources
      • Allows you to continue to use existing film cameras, mounts, etc.
      • Batch capabilities
      • Digital correction software
      • Multi-format—negatives, Kodachromes, glass slides, APS
    • Disadvantages
      • Can be expensive investment if scanner is uni-format
      • Fewer interface options, but this is changing
  • Film Scanners
    • Nikon Super CoolScan series
      • IV ED (2900 DPI, USB, ICE/ROC/GEM)
      • 4000 ED (4000 DPI, Firewire, ICE/ROC/GEM)
      • 8000 ED (4000 DPI, Firewire, ICE/ROC/GEM)
    • Minolta Dimage Series
      • Scan Dual II (2820 DPI, USB)
      • Scan Elite II (2820 DPI, USB/Firewire, ICE/ROC/GEM)
      • Scan Multi Pro (4800 DPI, USB/SCSI/Firewire, ICE/ROC/GEM)
    • Canon CanoScan Series
      • FS2720OU (2720 DPI, USB, FARE)
      • FS4000US (4000 DPI, USB/SCSI, FARE)





  • Flatbed scanners
    • Technology
      • Scanning technology varies greatly among these scanners
    • Advantages
      • Low-cost (high-end prosumer ~$1500)
      • Multipurpose (transparency/film adapters)
      • Multiple interfaces
    • Disadvantages
      • Lower native resolution (most @ 600ppi)
        • However, newer (higher-end) models scan at 2400ppi (prints an 8x12 at 300 dpi)
  • Flatbed Scanners

Epson Expression Microtek ArtixScan 2500f

2400 PHOTO Scanner

Canon DF2400UF CanoScan Scanner

  • Drum Scanners
    • High-end professional prepress digitizers
    • Can handle any size media (35mm to poster-size)
    • Scan from 4,000 to 10,000 dpi
    • Very expensive (>$10,000) and not necessary for most scientific work
processing editing
  • Software
    • At time of capture
      • Scanner interface
        • Can significantly add time to the capture process
    • Post-capture processing
      • Manual
      • Batch
    • Ethics of digital image manipulation
      • Still somewhat a gray area
processing editing26
  • Software
    • Photoshop products
      • Photoshop
      • Photoshop LE
      • Photoshop Elements
    • PaintShop Pro
    • Corel PhotoPaint
    • ACDSee
processing editing27
  • Batching images
    • Allows the user to automate image editing process
    • Functionality of PhotoShop batching is nice but may not be worth the cost—especially if paying retail
    • Other batch programs exist to allow the same functionality
      • Paint Shop Pro has batching features
      • BatchImage products (
      • Recommend Eyebatch from Atalasoft ($39.95) (
  • Focus on file storage rather than on temporary storage specific to capture device
    • Technology is rapidly changing at the device level
      • CompactFlash, Microdrives, Portable Devices
      • Fact is that for most pathology applications, the capture device is fixed and thus less dependence on these temporary devices
    • Relatively static in terms of permanent/archival storage over the last several years
      • Hard drives and CD-R/CD-RW (falling prices) are the standards
      • DVD technologies are still emerging, but are rapidly replacing CDs
  • Detached
    • Removable storage options
      • CD-R/CD-RW
      • DVD
      • Removable Hard Drive
      • Other (like Iomega Peerless)
  • Online
    • Fixed solutions
      • Hard drive
  • CD-R/CD-RW
    • Standard archival technology in current use
    • If you plan on capturing more than a few images, you need to invest in this technology
    • Advantages
      • Cheap hardware—under $100 for the latest, fastest drives (48x) (last year was $200 @ 24x)
      • Cheap media—<$.50 per 700Mb CD-R disk ($.75/Gb)
        • Each holds about 28 25Mb images or 158 4.4Mb images
      • Multiple back-ups easily made
      • Portable to almost any computer
      • Sturdy and not prone to failure
  • What about DVD technology?
    • The promise
      • Media at CD-R prices (eventually) with 6 times the storage capacity
        • 700Mb CD-R vs. 4.7 Gb per DVD-R
        • Currently, <$5 per DVD blank (~$1/Gb vs ~$.75/Gb for CD-R)
    • Drawback: No standard has yet emerged
      • Like VHS vs. Betamax, competing technologies (DVD-RAM, DVD-R, DVD-RW, DVD+RW) have not standardized
    • Drawback: Software has still not matured
    • Drawback: Speeds are climbing fast (standard is 1x burner, 2x available, 4x due soon)
      • 1x burns in about one hour
  • Hard drives--fixed
    • 60Gb drives (ATA100/7200rpm) are available around $100 ($1.75/Gb)
      • Hold 1500 25Mb images or ~9,000 4.4Mb images
      • If you don’t need the full-size image online, you can more efficiently store a smaller-sized copy online and keep the original archived to CD-ROM
      • We store images online as 792x528x24b uncompressed TIFFs at a file size of ~1.2Mb
        • At this size, we can store over 30,000 images per 40Gb HDD
  • Hard Drives as Removable Storage
    • We’ve found this to be a great compromise
    • Kits are available beginning at ~$15
      • Fixed portion that fits into a full drive bay
      • Removable tray that contains hard drive
      • Metal vs. plastic
      • With and w/o fans
  • Our storage workflow
    • Scan images at “capture” workstation onto a removable hard drive
    • Hard drive relocated to “burner” workstation where CD-ROM or DVD-R archive is made of the original scans
    • Hard drive relocated to “imaging” workstation where images are batch-processed
    • Depending on quality/needs, images can be archived again to CD-ROM at this point or manually processed and then archived
  • Storage workflow continued
    • Once images are in final state and archived to CD-ROM or DVD-R, the “full-size” (1500x1000) images are batch-resized on the original removable hard drive, thus overwriting the original files
    • These resized (792x528) images are then transferred to our online storage drives for network/Web usage
    • If at any point along the way the process is interrupted, the removable hard drive can be set aside without tying up online storage resources
  • File format considerations
    • Compression or not?
    • ***Paper?
local management
Local Management
  • Issues
    • Acquisition method
    • Cost (TCO)
      • Purchase vs. license
    • Proprietary* storage vs. open standard formats
      • Don’t get stuck with your images in their format
    • Metadata
    • Search capabilities
    • Scalability
local management39
Local Management
  • Too many software solutions to cover here
  • Our personal favorite is ACDSee
    • Low-cost ($99 for the most feature-rich version)
    • Searchable database (flatfile for easy access)
    • Built-in image editing and batching
    • Output HTML
    • PDA version (including editing!)
  • Many more listed/reviewed at
network management scalable solutions
Network Management/Scalable Solutions
  • Canto Cumulus
    • Local management ($99), workgroup, and full-scale server solutions
    • Add-ons available for personal edition to publish live to the Web or to create CD-ROM distributables
  • Extensis Portfolio
    • Local management ($199) up to full-scale server solution ($2500) (SQL/Oracle)
    • Create distributable CDs (with embedded user interface)
    • Personal edition includes a web server plug-in for Mac and Windows that allows you to dynamically publish the contents of your images on the Web
packaged solutions
Packaged Solutions
  • Vendors in the Exhibit Room
web based delivery
Web-based Delivery
  • Focus on software solutions specific to Web-based (can be intranet, also) delivery of image collections
    • Solutions based upon resources available, IT strategy, experience, initiative, desired outcome, etc.
      • Infinite combination of these variables complicated by an infinite possibility of solutions
    • Our experience has been that the only satisfactory solution is internally developed
      • I’m the developer and I’m still never satisfied
      • That’s where Perl comes in
    • Probably not going to solve your problem today even if I had all day just to show off solutions
      • Hopefully can spark some ideas
      • Always consider your IT guys—or you may reconsider
web based delivery43
Web-based delivery
  • WWW-Photo Sharing Services
    • Most simplistic, low-cost solution
    • Either free or for a small-fee, these services allow you to upload images on a remote Web-site
      • Depending on the service, images can be organized, annotated, and even edited online
      • Some services allow you to secure images behind passwords that you can control and distribute
      • Some of the services are tied to software that you can download and install on your local computer; you set everything up locally and then submit the result to the Web site with the push of a button
        • For example, ACDSee SendPix Service
web based delivery44
Web-based delivery
  • Advantages
    • Low-cost and low learning curve with high-tech result
    • Most sites have built-in security measures to protect your images
  • Disadvantages
    • Loss of control
    • No guarantee service will continue to be there
      • Time lost for online configuration
  • Case-study
    • Telepathology: Sate Hamza, MD
web based delivery45
Web-based delivery
  • Static-content solutions
    • Software installed locally that allows you to combine images and text in a Graphical User Interface and then produces a static HTML output that can be loaded onto a Web server
      • Too numerous to mention; often combined with local image management software packages
    • Advantages:
      • Full-control of output
      • Great for small, static solutions
    • Disadvantages
      • May require manual intervention
      • Usually no remote access for authoring
      • Not the best solution for multiple authors
web based delivery46
Web-based delivery
  • Dynamic (database-driven) solutions
    • High-end solutions
      • Scalable solutions mentioned earlier
      • Packaged solutions mentioned earlier
      • Enterprise solutions
    • Advantages
      • Robust
      • Continued support and development (as long as company stays afloat)
    • Disadvantages
      • Cost (including continued licensing costs)
      • Loss of control
      • Loss of configurability
      • May get stuck with proprietary solution
web based delivery47
Web-based delivery
  • Dynamic (database-driven) solutions
    • Home-grown solutions
      • In-house development of product for a specific purpose
      • Walk around and look at the E-posters/look at scientific session abstracts and talk to the people designing and developing these projects
    • Advantages
      • Low-cost (programmers work for pizza)
      • Solution is specific to need and usually reconfigurable
      • Sense of pride
    • Disadvantages
      • High-cost (support, failed attempts, labor costs)
      • May be limited by abilities of staff (who may move on)
      • Sense of despair
      • May open the floodgates of user requests for which you may not be prepared
web based delivery48
Web-based delivery
  • Dynamic (database-driven) solutions
    • Open source, non-proprietary solutions from small developers
      • Independent software houses develop low-cost solutions that are highly configurable by your in-house staff (if necessary)
    • Advantages
      • Low-cost ($0 to hundreds of dollars)
      • Support (may not even be necessary if open source)
      • Configurable (either pay for customization or do it in-house)
      • Usually scalable
      • Non-proprietary
      • Little loss if abandoned later (data on back-end in ASCII or standard database format)
      • Installation services/remote hosting usually cheaply available
      • Cross-platform (often by being browser-based solution)
web based delivery49
Web-based delivery
  • Dynamic (database-driven) solutions
    • Disadvantages
      • May require technical knowledge at your end (like knowledge of servers/Perl/HTML/database syntax)
      • May not have same level of support as with larger company (but you may be surprised!)
      • Your needs may outgrow the scalability of the solution
      • You may need to purchase/support/integrate several pieces of software to fully implement your solution
perl centered web based delivery
Perl-centered Web-based delivery
  • What do I need/need to know?
    • Network
      • Local Area Network (LAN) for internal solutions
      • Internet connection for WWW solutions
    • Web server
      • Not a piece of equipment (though it may be), but a piece of software that runs on a piece of equipment
        • Any PC can be turned into a Web server in a matter of minutes
      • Popular server software includes:
        • Apache (both *nix and Windows versions)
          • Free multi-platform solution, but no direct support
          • Most popular Web server software
        • IIS (Windows only)
          • Free with WindowsNT/2000
          • Familiar interface for the *nix uninitiated
perl centered web based delivery51
Perl-centered Web-based delivery
  • What do I need/need to know?
    • Perl or PHP
      • Scripting languages with an “interpreter” installed on the Web server to execute the commands
      • Free and cross-platform
      • Very similar in syntax and functionality
        • PHP is newer, easier to learn than Perl, and most scripts are open source
        • Perl is more well established (lots of code available) and more powerful but many scripts must be purchased (but are still mostly modifiable)
      • Some Web-based image delivery solutions require free add-ons to Perl or PHP to add functionality
perl centered web based delivery52
Perl-centered Web-based delivery
  • What do I need/need to know?
    • Database back-end (maybe/maybe not)
      • Depending on whether the delivery program you use requires it OR the size of your dataset requires it, you may be able to avoid the need for a database backend
        • Many programs only operate with flat file backends, which are character-delimited text files—e.g., an Excel-created comma-delimited spreadsheet
        • The data is ASCII text and easy to read/backup/manipulate directly
      • Database backends provide increased speed, reliability, and security
        • MySQL is the most popular and most widely supported
          • FREE, cross platform, open source relational database management system
          • Special (free) tools are needed for managing the database and editing/manipulating data
perl centered web based delivery53
Perl-centered Web-based delivery
  • Thus far:
    • Assuming you have a network (which means you have computers), you need
      • Free Web server software
      • Free script interpreter (Perl, PHP, or both)
      • +/- Free Perl/PHP-compatible database backend like MySQL
    • Did you say “free”? Can the good luck continue?
      • Maybe, maybe not
      • Now you actually need a program to put all these tools to work—many are indeed free
      • Most, however, are minimal in price (<$500 w/ most $100-$200—ask about educational discounts, as well)
        • C’mon, you looked so excited just a few lines up—we’re only talking about a month’s worth of lattes at Starbucks
perl centered web based delivery54
Perl-centered Web-based delivery
  • What next?
    • Consider needs
      • Size
        • Do you need a scalable solution or do you want to start big?
      • Speed
        • Related to size in some sense
      • Backend
        • Related to size, speed, and program support (you might have to do it even if size and speed needs don’t dictate it)
      • Security
        • Built-in user management vs. server-based security (or both)
      • Interface: search, browse, or both
        • Programs usually do one or the other better
      • Administration
        • Multi-user or single user
      • Upload capability
        • Via Web interface or file system access
      • Batch capability
        • Of text and/or images
      • Miscellaneous
        • Image server capability: on-the-fly watermarking, resizing, multi-format image support
perl centered web based delivery55
Perl-centered Web-based delivery
  • What next?
    • Find the best program for you (or one you can make the best)
      • Word of mouth
      • Online script repositories/review sites
      • Comparisons offered on product sites/from product representatives
perl centered web based delivery56
Perl-centered Web-based delivery
  • What follows is our word-of-mouth run-down of what we think are the best of the best solutions
    • Show some sample implementations (ours where possible)
    • Discuss some power tools to add extra functionality
      • Image server technology
      • Virtual microscopy tools
      • Thesaurus add-on
perl centered web based delivery57
Perl-centered Web-based delivery
  • Products from Gossamer Threads (
    • DBMan
      • Perl-based database program (not

image-specific, but implementable)

      • Primarily a search interface, but browse features can be implemented
      • Older flat file version ($100) and newer SQL version ($350)—scalable
        • We use it for our digital library of >40,000 images—started with flatfile and scaled up around the 15,000 image mark
        • Still use flatfile for GRIPE Digital Library of images/questions
      • Built-in user management for security (and/or use server-based security)
      • Easy set-up (but they will do a remote installation for a fee)
      • Built-in single or multi-image Web upload or link directly to images
      • Example:
perl centered web based delivery58
Perl-centered Web-based delivery
  • Products from Gossamer Threads (
    • Links
      • Perl-based database program (same as DBMan, just a different interface)
      • Primarily a browse interface with search features
      • Older flat file version (free for nonprofits/$100) and newer SQL version ($450)—scalable
        • We are currently creating a database of cases containing images for use in small-group based learning (students construct cases via a template and select images from our database to enhance the cases)
      • Built-in user management for security (and/or use server-based security)
      • Easy set-up (but they will do a remote installation for a fee)
      • Built-in single or multi-image Web upload or link directly to images
      • Dynamic or static delivery of content
      • Example:
perl centered web based delivery59
Perl-centered Web-based delivery
  • ImageFolio (
    • Perl-based image (and other files) management system
    • Primarily a browse interface with search features
    • Currently only available as flat file (but MySQL version in development)
    • Pro version (recommended) is $209 with $49 add ons (Batch processor, Shopping Cart, Upload module)
    • Built-in slideshow feature and shopping cart features e-mail option or mass download option for entire cart
    • Easy Web-based management with built-in admin security (but not user-side security—must use server-based security)
    • Create new pages by creating folders through Windows Explorer (on Windows systems) and then dropping images into the folder
    • We currently use for our autopsy database and for educational content
    • Easy set-up (but they will install it for a fee or host it remotely)
    • Example:
php centered web based delivery
PHP-centered Web-based delivery
  • PhotoPost (
    • PHP-based image management system
    • Primarily a browse interface with search features
    • Two MySQL versions (no flat file version)—GMS ($79) for basic one-user creation of galleries and Pro ($119) for multi-user “community-style” galleries with optional user-specific, password-protected galleries
    • Both versions offer image server support (more later) with on-the-fly resizing of images and dynamic watermarking
    • Easy Web-based management with built-in admin security and user self-registration
    • Built-in batch processing capabilities
    • Image commenting and rating system
    • Missing features: no shopping cart feature and no ability for a gallery creator to force images to be sorted in a certain fashion
    • Easy set-up (but they will install it for a fee)
    • Example:
perl centered web based delivery61
Perl-centered Web-based delivery
  • Special imaging tools (on-the-fly image resizing and watermarking)
    • ImageMagick
    • GD Graphics Library
    • Netpbm Graphics Utilities
perl centered web based delivery62
Perl-centered Web-based delivery
  • Image Servers
    • ACDSystems’ ImageShark
    • LeadTools Image Server
    • iSeeMedia’s Zoom Image Server
    • TrueSpectra Image Server
perl centered web based delivery63
Perl-centered Web-based delivery
  • Pan/Zoom Software for Virtual Microscopy Emulation (not real-time)
    • ACDSystems’ ImageShark
    • Xippix ImagePump
    • iSeeMedia’s Zoom Image Server
    • Zoomify
    • TrueSpectra Image Server
    • PowerPoint Presentation
    • Links directory to online resources for digital imaging
    • Case Study: PEIR Digital Library