Biomedical Imaging Resources

Nine Aperio Technologies, Inc. scanners are in service including, seven Model XT scanners Aperio XT, one Model OS oil scanner Aperio OS and one fluorescence Model FL scanner Aperio FL. Each scanner is controlled by custom imaging software running on a HP xw4400 workstation running Windows XP Pro. Each controller is powered by an Intel CoreDuo 6600 CPU @2.4GHz and is equipped with a PIXCI CameraLink video capture card. Scanner image resolution is .5 microns/pixel at 20X magnification and .25 microns/pixel at 40X magnification. In addition we have one Hamamatsu Model NDP 2.0 NanoZoomer bright field scanner.

• The LaCie NAS array consists of (3) network storage devices with a total capacity of 6TB.  Each LaCie Model 300961 NAS has a raw storage capacity of 2TB.
• An additional 750GB of storage space is available on DSR2 to store digital images in the event that the LaCie storage devices become unavailable.
• Should network connectivity be lost, each scanner control computer has 500GB disk space to store images.
• To provide storage for image files targeted by experimental image analysis algorithms and to share image file with local researchers, 2 enterprise level NAS devices are available.   An Adaptec SNAP 4500 Server provides a 330GB share and an Adaptec SNAP 520 Server provides a 2TB share.

OSC provides full weekly backups and daily incremental backups of all imaging data.

• WEBSVCS01: For the VIPER digital pathology review application, OSC provides an IBM X3455 1U server featuring 2 dual-core AMD 2.6 GHz Opteron processors (total of 4 cores), supported by 8GB of system memory and running RedHat Enterprise Linux 5.2, Apache, and Tomcat.   The VIPER box has 1GB network links to the DDN 9900.
• VMVIPER: a VMware-based virtual Windows box for Windows-based imaging applications and tools.  The virtual machine has the equivalent of one dual-core AMD 2218 Opteron processor running at 2.6 GHz, supported by 4GB of system memory and running Windows Server 2003 R2. The VMVIPER box has 1GB network links to the DDN 9900.   This machine is dedicated to support of a .NET test instance of the VIPER pathology review application and support of an imaging metadata database.
• VMVIPER2: a VMware-based virtual Windows box for Windows-based imaging applications and tools.  The virtual machine has the equivalent of two dual-core AMD 2218 Opteron processors running at 2.6 GHz, supported by 9GB of system memory and running Windows Server 2008 R2 Enterprise (64-bit OS). The VMVIPER box has 1GB network links to the DDN 9900.   This machine is dedicated to support of SlidePath digital imaging tools, including Digital Imaging Hub (DIH)  and OpTMA (TMA processing)
•  IA: a VMware-based virtual Windows box for Windows-based imaging applications and tools.  The virtual machine has the equivalent of two dual-core AMD 2218 Opteron processors running at 2.6 GHz, supported by 8GB of system memory and running Windows Server 2008 R2 Enterprise (64-bit OS). The IA box has 1GB network links to the DDN 9900.   This machine is dedicated to support of SlidePath TissueIA module (image analysis)
• VM2M, Linux DEV: OSC also provides hardware to support a general-purpose Linux development environment.  The support hardware is an IBM IntelliStation A Pro 6224 desktop featuring 1 dual-core AMD Opteron 2.2GHz Opteron processor, supported by 2GB system memory and two mirrored 160GB SATA drives.
  
  RedHat Enterprise Linux 5.2 is installed, supplemented by Apache, Tomcat, MySQL, and Java.
  
  This general-purpose Linux development environment is also supports the VM2M molecular genetics analysis application which stores gene chip experiment data and associated covariate data to support user-defined searches to effect molecular-based disease diagnosis.

• MS-HPC: OSC was a Linux-only shop until early 2008, when they installed the Microsoft High Performance Computing (HPC) cluster running Windows to support customers with applications requiring a Windows environment. The heart of this system is an IBM x3455 1U server featuring 1 dual-core AMD 2.4GHz Opteron processor, with 2GB of main memory, and a pair of 70 GB mirrored SATA drives for system software and swap space. The motherboard is capable of being upgraded to quad-core, quad-socket configuration, for a total of 16 cores. A link to the DDN 9900 provides storage for application executables and data.
  
  The HPC runs Windows Server 2008 supplemented with the Microsoft HPC package.
  
  The Research Institute imaging group is using the HPC cluster for image analysis, microarray gene chip experiment expression calculations, and microarray experiment pathway analysis.

VIPER, the Virtual Imaging Pilot EndeavoR initially began in January 2005 from the vision of Stephen J. Qualman as a pilot project to evaluate an automated pathology review process of both normal and diseased tissues for quality control purposes.
VIPER has now evolved into the Virtual Imaging for Pathology, Education & Research application to introduce imaging to other areas of emphasis at the Biospecimen Core. .   VIPER got its name from an acronym formed by the prime directives that guide the BIT initiative:

Virtual

Imaging - By utilizing whole slide imaging robots, the Biomedical Imaging Team is able to generate high quality virtual slides and make these images available via the VIPER application over the Internet. These “virtual” slides have essentially the same image quality and resolution as the same slide viewed through an optical microscope. Once the digital slide is available on VIPER, a common personal computer becomes the microscope. To facilitate the long-term storage and viewing of digital images, the VIPER Team has partnered with the Ohio Supercomputer Center (OSC). As a leader in computing and networking, the OSC provides a reliable high performance computing and communications infrastructure..

Pathology - The VIPER Team currently works with over one hundred pathologists representing the Children's Oncology Group, Gynecologic Oncology Group, The Cancer Genome Atlas Project and Nationwide Children's Hospital on multiple projects related to both pediatric and adult cancers, as well as non-cancerous diseases.

Education - Teaching sets are now available digitally via VIPER. Many of these teaching sets are focused on rare pediatric and adult tumors and have been generated at the request of leading cancer researchers in both the COG and GOG.

Research - The Biospecimen Core receives and processes over 165,000 specimens annually. Many of these specimens are processed into glass slides and evaluated digitally for quality control purposes. The BioPathology Center tissue bank has over 1 million unstained and stained slides in inventory that the BIT is systematically electronically imaging and adding to its imaging warehouse.   These images and associated metadata may one day support research queries that will help cure disease.

We encourage all visitors to review the VIPER application which can be found at http://viper.epn.osc.edu/viper/.