Digital Pathology Blog

What is your disaster recovery plan?

I was recently asked a question about digital pathology I had never given much thought to.

The question came out of a discussion relating to storage needs for digital pathology, particularly in a full adoption mode for 100% sign-out.  There are matters of capacity, live versus archival, storage time, redundancy, backups, etc...

A colleague of mine recently had his external 1 TB hard drive "crash".  Every powerpoint lecture, reams of research data, manuscripts, personal files & 25,000 mp3 files were thought to be lost.  He neglected to backup any of it obviously.  A commercial service restored the disk with everything but the music files.  We all know this happens routinely.  He did this only recently due to some constraints on enterprise servers and personal storage available on the institutional network and issues with file loss on shared folders with larger capacity.

A clock starts ticking the day you first use such a device that overtime will determine when some mechanical or software function will fail and loss is inevitable, in my opinion.  It has happened to me twice, both after about 3 years of use with varying sized drives and manufacturers.  Both times mirror drives caused no loss of any data.

In pathology we are careful to track what and how much tissue was collected, how may blocks are made, slides from those blocks, stains, recuts, slides sent-out, etc...

As we discuss storage needs and requirements for digital pathology we will have to think about similar issues and disaster recovery plans.

It made me think - what is our disaster recovery plan for stored tissue, wax blocks & glass slides?

I can't recall ever seeing a procedure or policy to address this issue at any institution. 

In case of fire, flood or hurricane what do you do?  What is your lab/institution's policy?

This hospital can trace its roots back to a tornado devastating the town.  The images can always be re-created assuming the real raw data is there to be had.

caBIG recent highlights

As caBIG(TM) aims to achieve broader engagement from organizations and institutions in the pharmaceutical, biotech, and commercial IT sectors, caBIG(TM) leadership will provide key resources to facilitate adoption of caBIG(TM) infrastructure, interoperability framework, and tools.

Issue 6 of caBIG(TM) Links highlights some of these resources, including informational materials and a recap of the November 8-9 caBIG(TM) Community Outreach Summit, which brought together key leaders in academia, patient advocacy, the private sector, and government. This issue also highlights some of the caBIG(TM)-enabled work that is led by Rakesh Nagarajan, M.D., Ph.D., at the Siteman Cancer Center at Washington University.

This month's issue features:

   * caBIG(TM) Seeks Broader Adoption within the Biomedical Community
     (http://cabig.cancer.gov/media/links/November_07/technology.asp)

   * Accelerating Research with Effective Biobanking
     (http://cabig.cancer.gov/media/links/November_07/people.asp)

To read this month's edition visit: http://cabig.cancer.gov/media/links/November_07/index.asp.

caTissue: Streamlining Biospecimen Management

Researchers who have easy access to relevant tools, biospecimens, and patient information can focus their work on finding cures for cancer and other diseases instead of being bogged down by the logistics of finding appropriate numbers and types of research specimens.

Unfortunately, many researchers may be limited by an inadequate availability of biospecimens relevant to their research and the arduous process of collecting enough samples outside of their own lab.
Read more

A new caBIG™ software tool called caTissue (developed by the Biomedical Informatics Facility at Washington University in St. Louis, MO) promises to greatly improve the way that biospecimens are catalogued, managed, and accessed—making it easier for researchers across the country to obtain a statistically significant number of specimens for use in experiments.

Traditionally, a researcher, or group of researchers at a specific institution, maintains their own dedicated biospecimen banks, using them for their projects as needed. But the challenge for researchers is that biospecimen repositories maintained by their institutions or partners may not encompass sufficient numbers of the appropriate high quality, clinically annotated biospecimens to achieve the most expeditious and rigorous results.

To facilitate the sharing of specimens among researchers nationwide, the Tissue Banks and Pathology Workspace of caBIG™ has spearheaded an effort to provide the open access caTissue tool to manage a centralized repository describing the location and types of biospecimens across multiple institutions.

The Biomedical Informatics Facility at Washington University in St. Louis led the development of this software and was instrumental in assuring its utility for researchers.

Read more on Why caTissue is important

Aperio Launches Advanced Digital Pathology Solution for Tissue Microarray Analysis and Research

Aperio Launches Advanced Digital Pathology Solution for Tissue Microarray Analysis and Research

From Aperio

National Cancer Institute and Netherlands Cancer Institute First to Adopt TMALab™ II Software

Vista, CA – July 16, 2007 - Aperio Technologies, Inc., the leading provider of digital pathology systems and services for the healthcare and life sciences industry, has launched TMALab II, the latest release of the company’s web-based digital pathology information management system, built specifically for researchers who use Tissue Microarrays (TMAs). With this release, Aperio continues to build upon its commitment to develop digital pathology solutions that meet the evolving needs of pathologists, researchers, and laboratories around the world.

TMALab II software enables researchers to analyze and manage hundreds of small tissue samples simultaneously in a meaningful way to facilitate leading research applications such as new biomarker validation, or discovering and dissecting molecular pathways. The software is the only web-based product that facilitates multi-user access and server-based image analysis, allowing numerous remote pathologists to collaborate on large TMA projects.

Researchers can easily retrieve all stains for any given core, and all cores for any given specimen. Additionally, the software provides links from any TMA core back to the original H&E slide cut from the corresponding donor block.

“Our first generation TMALab product has been successfully assisting scores of TMA researchers to streamline high-throughput tissue analysis in both the bio-pharma and cancer research arenas for many years,” stated Dirk Soenksen, CEO of Aperio. “TMALab II enhances the value of our digital pathology solution, sets new standards for ease of integration, and significantly expands data analysis and reporting capabilities for the TMA environment.”

Beta versions of the software have been successfully deployed at the National Cancer Institute in Bethesda, MD and the Netherlands Cancer Institute in Amsterdam. TMALab II is currently being used at the National Cancer Institute’s Tissue Array Research Program led by Dr. Stephen Hewitt. The initial project involves multiple slides prepared from 32 tissue microarrays. The TMA slides will be scanned using an Aperio ScanScope, annotated by a pathologist accessing the software via the Internet, and scored using quantitative image analysis algorithms. Additional projects have already been initiated using the platform to examine more than 75 stains on a single TMA.

TMALab II is fully integrated into Aperio’s patented linear array-based ScanScopeTM slide scanning system and SpectrumTM digital pathology information management software so that for the first time ever, researchers are able to manage digital whole slide- based projects along side TMA projects all within a single unified database containing specimen, digital slide, and TMA core information. In addition to data management and image retrieval, the software also enables server-based image analysis using any one of Aperio’s popular IHC algorithms or any compatible third party algorithms.

Issues with biorepositories

Dr. Ashokkumar Patel of the Case Comprehensive Cancer Center at Case Western Reserve University had an interesting posting on the Association for Pathology Informatics (API) Listserv recently dealing with issues on biorepositories.  A recent appeals court ruling has orderd that Washington University retains rights to prostate tissues collected by Dr. William Catalona (now at Northwestern University). 

Mention of the issues concerning Dr. Catalona's work have been published elsewhere.

There is also reference to a recent article in yesterday's St. Louis Post-Dispatch on the story.

For those interested, check out the website for the First World Congress on Pathology Informatics meeting in August.