The Biomedical Imaging Team provides several resources including imaging hardware, imaging services, slide conferencing, informatics and specialized projects such as the Virtual Imaging Pilot Endeavor (VIPER) and Virtual Microscope to Microarray (VM2M).
Creation of digital images from glass microscope slides is accomplished by a digital slide scanner.
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.[hide]
Tissue specimens prepared as slides are digitally imaged, with digital image files stored in a hierarchical arrangement. Primary storage is provided by LaCie NAS devices. Alternative storage is provided first by an internal disk share on DSR2, then by internal disk share on individual scanner control computers.[read more...]
Image files that meet quality standards are moved to the Ohio Supercomputer Center (OSC) for long term archival. OSC provides 50 TB of storage on a DataDirect Networks (DDN) S2A9900 Silicon Storage Array featuring 100TB of total storage capacity.[read more...]
OSC provides full weekly backups and daily incremental backups of all imaging data.[hide]
In collaboration with researchers on practical application of digital imaging, the Ohio Supercomputer Center (OSC) also provides a number of computing resources.[read more...]
The VIPER Viewing Station is a high-end Dell OptiPlex GX620 computer system consisting of: Pentium 4 650/3.4 GHz processor, 4 GB of 533MHz DDR2 memory, integrated video card as well as a FireMV 2400 128 MB DDR PCI Multi-view Graphics Card, (3) Dell Ultrasharp FP flat panel LCD monitors on a triple-monitor desk stand, and (2) 250 GB SATA hard drives.[read more...]
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:
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/.