Using Virtual Slides in Medical Education with the Virtual Slice System. Jack Glaser, President MicroBrightField, Inc.

Transcription

1 Using Virtual Slides in Medical Education with the Virtual Slice System Jack Glaser, President MicroBrightField, Inc.

2

3 Advantages of Virtual Slides Overview 0.08x Single section 0.63x Entire 2 x3 inch slide scanned with a 20x objective (~300x absolute mag). It is not possible to see this large a field-of of-view with a standard microscope. Even a single section overview is impossible with a microscope Multiple levels of resolution are available from a virtual slide Anatomic detail 5x Cellular detail 20x

4 Key instructional benefits The images are of highest quality and represent all modalities of optical microscopy Image collections can be updated as new material becomes available Images can be shared with other institutions Material can be used for both instruction and testing Slides can be accessed from outside traditional lab times

5 Key Economic Benefits Reduces or eliminates the need for microscopes No more replacing lost or broken slides Reduces need for lab space

6 Virtual Slide Technology Components

7 Virtual Slide Acquisition Methods 1. Montage Scanning Can be used with existing microscopes Can obtain images from other forms of microscopy, i.e. fluorescence More Economical 2. Strip Scanning Fast Scan Speed

8 Montage Scanning Motorized stage and digital camera used to acquire an image at each field-of of-view

9 MBF Scanning Technology Acquisition with Virtual Slice technology Acquisition with standard research microscope Video or digital camera Microscope with high quality optics Motorized stage and stage controller Computer with MicroBrightField software and video capture card

10 MBF Scanning Technology Acquisition with Virtual Slice technology Many illumination techniques can be used Brightfield, darkfield, fluorescence, etc. Fluorescently stained (GFP) mouse brain acquired at 40x

11 MBF Scanning Technology Acquisition with Virtual Slice technology Many slide formats can be used Such as 1 x3 slides, 2 x3 slides, large format slides, even an entire section of a human head

12 Virtual Slide Technology Acquisition with Virtual Slice technology Acquisition with standard research microscope Each field-of of-view acquired in sequence, seamlessly stitched to adjacent fields. Amount of blending and matching controlled by the user Extremely large image files are generated Typical: Digital acquisition of 40 x 40 fields of view with 40x objective (~7 x 7 mm piece of tissue) Each field is 4MB, total uncompressed image size ~6.5GB Challenging: Acquisition of entire human cerebellum with 20x objective Uncompressed size: 97.5 GB How to view, manage, and distribute such large files?

13 Using an Effective Virtual Slide Viewer An effective virtual slide viewer has the following attributes: The virtual slide may be viewed at any magnification, up to the magnification of acquisition The virtual slide may be dynamically explored in any region at any magnification Multiple people can view a slide simultaneously The functionality is familiar to users of traditional microscopes Virtual slides stored in various file formats can be seamlessly viewed

14 Virtual Slide Storage Formats Virtual slides can be stored as a single large file or as a multitude of smaller files Advantages of a Single Large File Can use industry standard file formats Less complex to manage Advantages of Multitude of Files?

15 File Formats for Virtual Slides Problem Large storage requirements Solution Use Proven Image Compression Techniques Flashpix format (JPEG) Zoomify (JPEG) MrSID (Wavelet) JPEG2000 (Wavelet) Note: many popular formats have size limitations i.e. the limitation of TIFF format is 2GB

16 File Formats for Virtual Slides Compression Formats -- Wavelet vs. JPEG Wavelet compression allows for greater compression at greater computational expense (slower to create, slower to view) Typical Wavelet Compression: 6.5GB 125MB JPEG compression is faster and less computationally intense Typical JPEG Compression: 6.5GB 550MB 550MB

17 File Formats for Virtual Slides Is a proprietary file format a potential problem? pro pri e tary 1 : one that possesses, owns, or holds exclusive right to something; specifically 2 : something that is used, produced, or marketed under exclusive legal l right of the inventor or maker; specifically : a drug (as a patent medicine) that is protected by secrecy, patent, or copyright against free competition as to name, product, composition, or process of manufacture Merriam Webster Nearly every image file format, i.e., TIFF, BMP, GIF, etc. is by definition #1 Files in category #2 might be a problem

18 Viewing Virtual Slides Problem: Large files are sluggish to load in image programs such as Photoshop, Corel, etc. A 1GB file typically takes >5 minutes to load Solution: We developed an innovative web-based based viewer Only the requested field-of of-view is transmitted Fast, dynamic viewing of slides

19 File Formats for Virtual Slides Problem Retrieving select data from a large traditional image file is time consuming Solution Images are stored in a multi-resolution pyramidal format A multi-resolution file format allows images to be stored at different resolutions r for different purposes. Each resolution is divided into 64 x 64 blocks. Within a block, pixels can be either uncompressed, JPEG compressed or single-color compressed. Image is downsampled during storage allowing for fastest visibility.

20 Virtual Slide Viewer Standard Browser Window Zoom Tools Slide Area Magnification control Thumbnail of Entire Slide Text Information about Slide Current View Panning Tool

21 Virtual Slide Viewer Viewer is a Java applet, works on multiple platforms without need to download plug-ins Windows Explorer 5.0 and higher MacOS 10.2 and higher Linux Solaris Easily viewed on a typical desktop computer 128 MB RAM 500 MHz processor Win98 or later The images reside on a server computer

22 Internet Virtual Slide Viewer Server sends only the selected field-of of-view Made up of many 64x64 fields (~1KB each) Close up of macro view shows extensive compression within a single block Many blocks ~5µm/pixel, 1 block When a small, high magnification field-of of-view is requested, a group of blocks from a more detailed level of the pyramid are sent. ~0.16µm/pixel, Many blocks

23 Internet Virtual Slide Viewer This slide view shows completed blocks as they load. Previously viewed blocks are cached for repeat viewing

24 Internet Virtual Slide Viewer Example: Viewing a virtual slide of a human jaw (Next Generation of the Visible Human feasibility study)

25 Virtual Slide Viewer University of Iowa medical histology instruction CSULB Avian brain atlas creation Our Java viewer applet is easy to insert into custom Web pages for maximum flexibility JSP, ASP, PHP, etc. Ohio State University tissue microarray visualization

26 Internet Slide Viewer What kind of Internet connection is required? Typical download times for a single field-of of-view: LAN T1 DSL/Cable Dial-up Modem 0.9 seconds 1.5 seconds 4 seconds 1 minute

27 Enhancements with Virtual Slide Viewing In addition to viewing at multiple magnifications, the virtual slide platform allows for many enhancements to the microscopic slide material: Store locations on a slide Create graphical overlays Store overlays with specific locations Store text descriptions of the slide or a specific location on the slide Create hyperlink labels Perform quantitative measurements of slide material

28 Virtual Slide Viewer Macro View, Pan and Zoom tools Text information about the slide, hyperlinks, and links to specific views Simplified viewer window provides easy access to navigation tools and slide information

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

30 Virtual Slide Viewer Customizable Labeling tools Types of Labels Text Arrows Text and Arrows Monocle Contours Full range of Colors Customizable Fonts Link to any Magnification Analysis of contour sizes

31 Virtual Slide Viewer Problem Using traditional labeling techniques makes labels appropriate for one level of zoom only Solution Labels stored separately from image files in vector format

32 Virtual Slide Viewer Labels added in separate layer from the image If label is part of the image, zooming in makes text inappropriately large Labels shown appropriately sized for viewing when labels are stored in an independent layer

33 Virtual Slide Technology Problem How to store and manage large numbers of virtual slides? Solution Development of interoperable slide management system (database)

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

35 Virtual Slide Management Database Storage What are the demands of the server? Minimum Hardware: 1 GHz Processor 1 GB RAM Windows 2000, Linux, Solaris OS Architecture is scalable, allowing for division onto multiple machines, web server and image server

36 Virtual Slide Management Problem Many students need to access the slides at one time Solution Load balancing servers automatically distribute the computational demands to other computers

37 Virtual Slide Management Server Load Balancing One server 30 simultaneous users With Virtual Slice load balancing capability servers can handle unlimited users

38 Examples of Integration of Viewer and Database Composing a Quiz Instructor finds area on slide, outlines region, types in question and answer. All information is maintained in the database.

39 Examples of Integration of Viewer and Database Taking a Quiz Student later is automatically taken to the area on the slide, and a sees the question. The student may enter her answer.

40 Examples of Integration of Viewer and Database Self Quizzing The student may test their knowledge on their own. The student sees the answer after clicking on the Show Answer button.

41 Examples of Integration of Viewer and Database Side by Side Slide Comparison

42 Color Balancing and Modification White balance and color adjustments may be made

43 Alternative Virtual Slide Storage Technology Virtual Slide Storage Virtual slides and viewer can also be set up on a single machine, or distributed on a CD. Limitations: Number of slides limited by hard drive space or CD space No interactivity Difficult to update Advantages: No network needed Convenient where high-speed Internet is not available

44 How does a professor use a virtual slide? Selects the slides to be used in the class. Edits and revises the slides to insert markers, annotations, comments, and questions. Links the slides to other didactic material to create a unified course presentation.

45 How does a student use the virtual slide? Logs in to the web site or local server from their computer Selects the course material or the slides of interest Navigates through the slide at his/her discretion, observing the morphology, noting comments, answering questions Asks questions to teacher Logs off

46 The Future of Virtual Slides Increase in image quality, automation, and acquisition speed Creation of 3D virtual slides (multiple focal planes) Increase in content quality available on web Archived collections of pathological specimens Archived collections of research specimens Widespread use of virtual slides in clinical use

47 Conclusion Virtual slide technology is a rapidly emerging field enabling unprecedented availability for accessing microscopic specimens Virtual slide viewers enhance the functionality of microscope with ability to store locations, add annotations, link to other sites and information. In many situations, virtual slides have distinct advantages over traditional glass slides. Current technology makes the use of virtual