Biomedical Imaging Team Resources :: The Research Institute at Nationwide Children's Hospital

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Behind the Scenes: Virtual Microscopy at our Research Institute

Biomedical Imaging Resources

The Biomedical Imaging Team provides several resources including imaging hardware, imaging services, slide conferencing, informatics and specialized projects such as the Virtual Imaging for Pathology, Education and Research (VIPER).

Scanners

Creation of digital images from glass microscope slides is accomplished by a digital slide scanner. Nine Aperio Technologies, Inc. scanners are in service including, five Model XT scanners Aperio XT, two Model AT Turbo, 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.

Local Storage Capacity

Tissue specimens prepared as slides are digitally imaged, with digital image files stored in a hierarchical system. Primary storage is provided by a custom NAS device directly addressed by the individual slide scanner control computers. Secondary backup storage is provided first by an internal disk share on DSR2, tertiary backup storage by an internal disk share on the individual scanner control computers.

The custom NAS (“SStorage”) consists of 4U rack chassis housing a motherboard populated with a AMD processor, running Windows Server 2008R2, complemented by a RocketRaid RAID controller managing (5) 2TB WD Black hard drives in a RAID1+0 configuration with a total capacity of 4TB with a hot spare ability. SStorage is also home to (4) 3TB Western Digital Green hard drives running in RAID5 with an effective storage of 9TB. This is a slightly lower speed setup that is primarily used for archiving.

An additional 750GB of storage space is available on the DSR2 to store digital images in the event that the custom storage device becomes unavailable.

Should network connectivity be lost, each scanner control computer has 500GB disk space to store images.

To provide shared storage for image files targeted by experimental image analysis algorithms and to share image file with local researchers, 2 NAS devices are available on The Research Institute enterprise network. An Adaptec SNAP 4500 Server provides a 330GB share and an Adaptec SNAP 520 Server provides a 2TB share.

Off-Site Storage Capacity

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. The file structure implemented on the DDN is GPFS.

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

Local Computing Resources

  • HPC Cluster: In 2012 the BPC Imaging Core installed an HPC cluster consisting of selected off-the-shelf hardware custom assembled by Advanced Clustering Technologies. Main components include a head node and (3) compute nodes.

The head node: 2U Chassis, 2 redundant 660 Watt powers supplies, 8x8GB=64GB DDR3 ECC Registered RAM, 2x240GB Solid State Drives in RAID1, 500GB Western Digital SATA3 Velociraptor, 2xIntel Xeon E5-2670 (8 Cores @ 2.6GHz)

The head node manages the overall jobs, dividing compute demands across resources (both CPU and GPU) on the compute nodes, compiling final results using Windows Server 2008R2 HPC edition and SQL Server 2008R2.

The compute nodes (3): 5U Chassis, ASUS 1200 Watt power supply, 16x8GB=128GB DDR3 ECC Registered RAM, 480GB Solid State Drive, 2xIntel Xeon E5-2670 (8 Cores @ 2.6GHz), 2xNVIDIA Tesla C2075 6GB GDDR5 parallel processing cards.

The imaging HPC cluster runs custom image analysis algorithms that inspect each image generated by the slide scanners for image defects, most notably stripe mismatches caused by image processing errors and blurs often caused by tissue folds.

  • RESC3-DSR2: DSR2 is a Dell R710 2U rackmount server running Windows Server 2008R2 SP1. DSR2 includes a (4) 450GB SAS drives in a RAID0 array with a total capacity of 840GB. The array is partitioned into a virtual 80GB drive for the OS, and a virtual 733GB drive for data.

The primary function of this server is to manage all the slide scanner control computers. It also hosts some Aperio image processing tools.

Off-Site Computing Resources (OSC)

In collaboration with researchers on practical application of digital imaging, the Ohio Supercomputer Center (OSC) also provides a number of computing resources.

  • VIPER: 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, supplemented by Java 1.5, Apache Tomcat 5, and MySQL 5.0.77 (running on xio20 – a dedicated MySQLdatabase server). The VIPER box has 1GB network links to the DDN 9900 for access to the imaging storage share. This machine is the primary host for the web-based VIPER Pathology Review Application, serving up digital slide images, pathology reports, and editable electronic review forms.
  • VMVIPER: A VMware-based virtual Windows box for Windows-based imaging applications and tools. The virtual machine has the equivalent of (2) 6-core Intel X5650 CPUs running at 2.67 GHz, supported by 8GB of system memory, and 80GB of hard drive space to run Windows Server 2008 R2 Standard SP1 (64-bit). The VMVIPER box has 1GB network links to the DDN 9900. This machine is dedicated to support of a test version of VIPER.NET, Windows-based Aperio ImageServer, Aperio Digital Slide Conferencing, and hosting an externally-available Aperio Spectrum instance.
  • VMVIPER2: A VMware-based virtual Windows box for Windows-based imaging applications and tools. The virtual machine has the equivalent of (4) 6-core Intel X5650 CPUs running at 2.67 GHz, supported by 9GB of system memory, and 160GB of hard drive space to run Windows Server 2008 R2 Enterprise SP1 (64-bit). An additional 100GB of hard drive space is configured for data. The VMVIPER2 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 (2) 6-core Intel X5650 CPUs running at 2.67 GHz, supported by 8GB of system memory, and 150GB of hard drive space to run Windows Server 2008 R2 Enterprise SP1 (64-bit). The IA box has 1GB network links to the DDN 9900. This machine is dedicated to support of SlidePath TissueIA (image analysis) and perform database processing for SlidePath DIH.
  • 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 Java 1.5, Apache Tomcat 5, and MySQL 5.0.77 (running on xio20 – a dedicated MySQLdatabase server).

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 8500 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.

Pathology Review Station

Updated in 2012, the imaging Pathology Review Station is a high-end Dell OptiPlex GX790 computer system consisting of: Intel i5-2400 CPU @ 3.10GHz , 8 GB of DDR3-1600 memory, an Intel 82579 LM Gigabit network adapter, (1) 500GB hard drive for OS (Windows 7 Enterprise 64-bit) and apps, (1) 1TB hard drive for general data, (1) Dell DH-16ABS 16X H/H SATA DVD±RW, and twin ATI Radeon HD5450 Display Adapters driving (3) Dell Ultrasharp 2007FP 1600x1200 flat panel LCD monitors arranged on a triple-monitor desk stand.

Typically, one of the three monitors will display the web-based “VIPER” Pathology Review application, another display the pathology report (and/or electronic review form) downloaded from VIPER for the particular case under review, and the third display the digitally stored whole slide images downloaded from VIPER associated with the case under review.

Power Considerations

  • EMERGENCY GENERATOR: All imaging equipment plugs into UPS equipment which in turn plugs into electrical outlets configured to automatically switch over to emergency generator power in the event of commercial utility power failure.
  • Uninterruptible Power Supplies (UPS): DSR2, DSR3, SStorage, the HPC cluster, and all digital slide scanner control computers are powered directly from APC 2.2KW UPS systems. All systems are generator compatible and feature sine wave output for best compatibility with all load devices.
  • The combination of emergency generator backup and UPS devices provides the best possible assurance that production scanning jobs can finish without interruption.

VIPER

From the vision of Stephen J. Qualman VIPER, the Virtual Imaging Pilot EndeavoR initially began in January 2005 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.

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 and has allocated 50 terabytes of storage capacity for VIPER.

Pathology - The VIPER Team currently works with over one hundred pathologists representing the Children's Oncology Group, Gynecologic Oncology Group, South West 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.

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

Nationwide Children's Hospital
700 Children's Drive Columbus, Ohio 43205 614.722.2000