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Disease Markers 23 (2007) 459–466 459IOS Press

Utilizing virtual microscopy for qualitycontrol review

Nilsa C. Ramirez∗, Thomas J. Barr and David M. BilliterColumbus Children’s Research Institute, Center for Childhood Cancer, Columbus, OH, USA

1. Introduction

Virtual Microscopy (VM), the technique of digitiz-ing microscope slides with common objective magni-fications, may be equivalent to original glass slides onmicroscopes and will provide diagnostic image qual-ity. Based on this technology an automated patholo-gy review system can be designed in order to facilitatea more efficient quality assurance (QA)/quality con-trol (QC) review process. The Gynecologic Oncolo-gy Group Tissue Bank (GOGTB) is funded by the Na-tional Cancer Institute (NCI) and located at ColumbusChildren’s Research Institute in Columbus, OH Thecomplexity of the GOGTB operation requires a reli-able QC program that is accessible to multiple out ofsite/out of state reviewers on a regular basis, ideally 24hours a day, 7 days a week. In this setting, VM offers areliable and potentially cost efficient alternative to themore classical method of glass slide peer review pro-cess that involves time consuming and costly packagingand mailing of material.

The Virtual Microscopy Pilot EndeavoR (VIPER)(Fig. 1) pilot project automates the QC review processby allowing expert reviewers to remotely view digitalimages via the Internet. The VIPER system notifiesreviewers of new cases and allows reviewers to identifysignificant slides, complete cases, request accounts,andreset accounts automatically. VIPER also streamlines

∗Corresponding author: Nilsa C. Ramirez, M.D., E-mail:[email protected].

the process utilized by the GOGTB by assigning useraccounts, passwords, cases, and slides electronicallyand allows the GOGTB to administer review protocolsby the cooperative group and/or submitting institutions.The VIPER system was designed and developed aftera thorough analysis of the GOGTB workflow (Fig. 2).

Prior to implementing VM, the QC process requiredthat glass slides and paper forms be physically shippedbetween the GOGTB and the reviewing pathologistsresulting in extended QC review times and substan-tial shipping costs. VIPER facilitates translational re-search in gynecological cancer by providing a web-based pathology review and a digital archive of originalpathology material.

2. Pathology utilization

Pathologists have traditionally utilized microscopesto aid in the diagnosis and treatment of disease, butmodern image capture technology has provided newmethods to review specimens. Virtual Microscopy isthe technique of digitizing a glass slide with commonlyused objective magnifications producing a digital virtu-al microscope slide that can be viewed with a personalcomputer. A VM slide is the equivalent of the origi-nal glass slide on a microscope. It provides diagnosticdigital images (DI) of good quality, allowing users tonavigate and view the image at multiple magnificationsand at any time.

There are numerous benefits associated with the useof DI. Any tissue stained and prepared on a traditionalglass slide setting can be scanned. Staining methodsare variable, and include histochemical and immuno-histochemical stains. The tissue is available for rapid

ISSN 0278-0240/07/$17.00 2007 – IOS Press and the authors. All rights reserved

460 N.C. Ramirez et al. / Utilizing virtual microscopy for quality control review

Fig. 1.

N.C. Ramirez et al. / Utilizing virtual microscopy for quality control review 461

Fig. 2.

review once the electronic image from a master slideis created. This eliminates the need to ship glass slidesto multiple reviewers, and allows for images to be re-viewed simultaneously by multiple reviewers. Thisformat is extremely helpful when diagnostically diffi-cult cases or unique tissue findings (likely confined toa single tissue slide) are reviewed. Using VM reducesthe number of broken slides and lowers (or can eveneliminate) shipping costs. Digital annotations can beperformed on the images with no impact on the orig-inal glass slide. DI creates a retrievable database ofsubmitted material that can be used for confirmation ofeligibility criteria, creating a digital archive that doc-uments the original pathology material and quantifiesthe pathology images. The use of VM enhances theselection of research material, providing an on-line re-view of original material prior to an investigator select-ing or requesting tissue. DI can also be used to educatemedical and research professionals involved in researchand/or diagnostic tissue-based projects and as part of aquality control/quality assurance program. The objec-tive of the GOGTB is to fully-utilize this technologyby implementing an automated pathology review sys-tem to facilitate a more efficient and cost-effective QCreview process.

3. VM technology

Although several companies currently offer imagingproducts designed for use on glass slides we will focus

on the systems currently used by the GOGTB. Afternegotiating with several vendors, the GOGTB selectedAperio Technologies as the initial vendor for all digi-tal imaging of tissue specimens. Much of the decisionprocess was related to the line scanning technology andthe rapid scan times provided by the Aperio system.According to Aperio Technologies, “Line scanning is asignificant advancement in rapid, high resolution virtu-al microscopy. Line scanning is a superior methodol-ogy to image tiling. ScanScopescanners do not usea fixed-area camera to capture thousands of individualimage tiles but instead employ linear-array detectorsin conjunction with specialized motion control com-ponents, a microscope objective lens and customizedoptics.”

A variety of tools are required to successfully im-plement VM. These tools consist of both hardware andsoftware. The GOGTB currently utilizes both vendor-supported and custom-developed software as well asthe ScanScopeT2 patented linear-array slide scannerto fully deploy virtual microscopy into the GOGTBbusiness processes.

The main hardware element is the ScanScopeT2,a patented linear-array slide scanner, which is utilizedwith a 120-slide autoloader to provide the digitizationof entire microscope slides at high resolutions. Theseimages are then compressed and stored for later re-trieval. The use of a Virtual Slide Repository (VSR), ahigh-end computer that runs all ScanScopesoftwareapplications, provides temporary local storage of all


Fig. 3.

virtual slides created with the ScanScope. Imagesthat are temporarily stored on the VSR are then secure-ly transported via the SSH Secure Shell application tothe Ohio Supercomputer Center (OSC). The OSC cur-rently provides 10 terabytes of storage space in a se-cure Linux environment for storing and serving digitalimages.

There are multiple software components that are uti-lized with the T2 system. The first is the ScanScopeConsole (Fig. 3), provided by Aperio Technologies,that provides the user with an interface to the slidescanner. ScanScope Console allows the user to cus-tomize the scanner setup to satisfy a particular user’sneeds. This customization includes several routine op-tions such as the selection of the desired slide magnifi-cation, the number of focus points, and the area of theslide to be scanned. The Console also allows the user toconfigure more specialized features by providing userswith the ability to dictate data file formats, compres-sion amounts as well as create custom parameter setsfor specific tissue types.

Spectrum Information Manger (Fig. 4) is anothertool provided by Aperio Technologies to assist userswith integrating digital imaging into current businessprocesses. The application accesses a database thathouses vendor-provided fields and gives the user theability to store and organize custom fields. Spectrumintegrates with the ImageScopeTM allowing the userto view digital images and perform image analysis onthese images. Spectrum allows users to edit slide dataas well as manage slide images by sorting, filtering,searching, and removing data and images. All datacollected and stored in the Spectrum database can beextracted.

Virtual Slide Manager is software which is used withthe VSR for tracking slide data and managing the work-flow associated with the virtual slides. All slide data ismaintained and updated in a database table which pro-vides specific information about each slide includingassay information as well as customizable fields.

A very important software component of the over-all system is the ability for users to view the actual


Fig. 4.

slide image. As images are available for review at theOSC, the reviewers need a software viewer to view,pan and zoom the digital images. Current reviewersat the GOGTB utilize either the Aperio WebViewer(Fig. 5) or Aperio ImageScopeTM (Fig. 6) software toview digital images. Although both the WebViewerand ImageScopeTM viewers provide diagnostic qual-ity images additional functionality is provided by theImageScopeTM application.

The Aperio WebViewer allows the viewing of imagesthat are displayed on a web page and can be remotelyaccessed by most web browsers. Use of WebViewerdoes not require a download or plug-in and is primarilyused by Macintosh users. Aperio ImageScopeTM, aclient-side software package, is available only to users

with Microsoft Windows 2000 or Microsoft WindowsXP for viewing virtual slides. ImageScopeTM pro-vides additional functionality over WebViewer whichincludes authoring annotations, integrated image anal-ysis, digital slide conferencing, more convenient nav-igation options, and faster rendering of images. TheDigital Slide Conferencing (DSC), provided by Ape-rio Technologies, promotes collaboration by enablingmultiple reviewers to simultaneously and synchronous-ly view an image with ImageScopeTM and an internetconnection.

Currently the GOGTB uses the Digital Slide Studio(http://www.aperio.com) to compress raw data provid-ed by the scanner to make the file sizes more manage-able. File sizes vary by tissue size and desired magnifi-


Fig. 5.

cation; image data generated by linear-array slide scan-ners is generally large and requires data compressionto reduce the file sizes prior to making that data avail-able to reviewers. As the popularity of computer aideddiagnosis (CAD) has increased, issues related to imagecompressions has become much more challenging.

In an effort to facilitate the use of tissue microarrayswith VM the GOGTB utilizes TMALabTM (Fig. 7)which is a software component provided by AperioTechnologies. TMALabTM provides a graphical userinterface to assist users in locating and identify spotswithin a Tissue MicroArray. TMALabTM also allowsusers to open multiple spots simultaneously, pan andzoom spots, and compare stain intensity of the spots. Acomposite TMA can also be created by allowing usersto select spots from multiple Tissue MicroArrays. TheTMALab software is increasing in its use due to thelimited availability of consented human tissues. Tis-sue microarrays are now becoming more popular tomaximize use of these valuable tissues. Finally theTMALabTM provides the user with the ability to bothimport and export research data in a variety of formats.

The complete VM process also utilizes customizedsoftware developed by the GOGTB informatics group

to meet the workflow of the operations staff and thereviewers. Due to the complexity and variety of slidenames encountered at the GOGTB it became necessaryto create a simple application to interface with data filesexported from the Workflow Manager application. Thisrenaming software reads the exported Comma Sepa-rated Value (CSV) file and renames all files located inlocal storage to the preferred slide names and movesthese files to the designated location.

At the GOGTB all specimens must be reviewed byexpert pathologists prior to these specimens being madeavailable to researchers. Historically this process hasrequired that glass slides, pathology reports, and pa-pers be physically shipped to expert review patholo-gists to verify diagnoses provided at the patients localinstitution. The Virtual Microscopy Pilot EndeavoR(VIPER), an automated digital pathology review sys-tem, is a custom built application designed to replacethe historical review process.

The VIPER pilot project is designed to automatethe pathology QC review process by allowing expertpathology reviewers to remotely view digital imagesvia the Internet. The VIPER system allows the re-viewers to identify significant slides (i.e. those slides


Fig. 6.

Fig. 7.


imperative to making diagnosis and quality decisions),complete case review, request accounts, and reset ac-counts automatically. VIPER was custom-designed toallow GOG TB operations staff to not only assign useraccounts, passwords, cases, and slides, but also to ad-minister review protocols, per cooperative group, andper institution. VIPER was developed by the GOGTBInformatics Group utilizing various Linux-based tech-nologies including Apache Tomcat, Hypertext MarkupLanguage, JavaScript, JavaServer Pages, and MySQL.

To implement the VM technology, it was imperativeto objectively review the benefits and caveats of theVM, validate the technology, and implement VM intoto current staff workflow. VM facilitates translationalresearch in gynecological cancer by providing both aweb-based pathology review and a digital archive oforiginal pathology material submitted for confirmationof eligibility criteria in a retrievabledatabase. By utiliz-ing VM, the technique of digitizing microscope slides,the GOGTB is able to provide expert review pathol-ogists with digital images used for diagnostic qualityassurance. Building on previous experiences VIPER

further automates the pathology review process by al-lowing reviewers to securely review and identify clin-ically significant slides, complete cases, request ac-counts, and reset accounts automatically. The systemalso notifies the review pathologists by electronic mailof new cases.

4. Conclusion

VM will facilitate translational research in gyneco-logical cancer by providing both a web-based pathol-ogy review and a digital archive of original pathologymaterial submitted for confirmation of eligibility crite-ria in a retrievable database.

Acknowledgements

Aperio Technologies.

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