Acquisition and Use of Digital Images for Pathology Education and Practice APIII 2002 Peter G. Anderson, DVM, PhD Kristo

1. 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

2. 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 http://peir.net

3. Purpose • 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

4. Scope • 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—http://peir.net/apiii

5. Focus • 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

6. 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…

7. 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”

8. Acquisition • 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

9. Acquisition • 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

10. Acquisition • 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

11. Acquisition http://www.imaging-resource.com/TIPS/PRINT1/PRINT1A.HTM • 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

12. 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

13. Acquisition • 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

14. Acquisition • 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)

15. Acquisition • 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

16. Acquisition • 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

17. Acquisition • 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

18. Acquisition • 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

19. Acquisition • 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

20. Acquisition • 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)

21. Acquisition No ICE w/ ICE

22. Acquisition • 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)

23. Acquisition • Flatbed Scanners Epson Expression Microtek ArtixScan 2500f 2400 PHOTO Scanner Canon DF2400UF CanoScan Scanner

24. Acquisition • 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

25. 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

26. Processing/Editing • Software • Photoshop products • Photoshop • Photoshop LE • Photoshop Elements • PaintShop Pro • Corel PhotoPaint • ACDSee

27. Processing/Editing • 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 (http://batchimage.com) • Recommend Eyebatch from Atalasoft ($39.95) (http://www.atalasoft.com)

28. Processing/Editing

29. Storage • 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

30. Storage • Detached • Removable storage options • CD-R/CD-RW • DVD • Removable Hard Drive • Other (like Iomega Peerless) • Online • Fixed solutions • Hard drive

31. Storage • 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

32. Storage • 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

33. Storage • 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

34. Storage • 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

35. Storage • 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

36. Storage • 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

37. Storage • File format considerations • Compression or not? • ***Paper?

38. 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

39. 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 http://peir.net/apiii

40. 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

41. Packaged Solutions • Vendors in the Exhibit Room

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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)

49. 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

50. 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