GE Healthcare Life Sciences Locate Correlate Communicate IN Cell Miner High-Content Manager (HCM) Critical information at your fingertips
IN Cell Miner HCM Managing your high-content data IN Cell Miner HCM from GE Healthcare Life Sciences provides you, and others within your organization, the capability to annotate, archive, retrieve, and store high-content images, so you can be confident that the value of your data is captured and realized. IN Cell Miner HCM is a relational database that can be used as a stand-alone system for a small workgroup, or can be snapped into your organization as a seamless complement to your existing system. Based on the stable and industry-proven EMC Documentum platform, IN Cell Miner HCM incorporates open standards, and is easy to use, easy to integrate, and completely scalable. Organize, find, share, compare, and publish your data quickly and easily.
Managing the data mountain High-content analysis (HCA) provides information-rich, quantitative insights into cellular events and processes, but increasing productivity creates new requirements for data management. IN Cell Miner HCM meets these challenges by providing on-demand access to and analysis of the increasing data volume from your HCA projects. HCA measures biochemical and morphological changes in cells both rapidly and accurately. However, each year, HCA/HCS systems, such as IN Cell Analyzer can produce: 38 TB of data 12 million images 30 billion measurements from individual cells Once annotated with detailed experimental conditions, this mountain of interconnected data becomes a valuable asset for basic research and drug discovery that can be mined for an understanding of cellular function or drug action. Meta-data Provide context Quantitative results Drive decisions Images Revisit raw data Fig 1. The HCA data mountain. Images make up most of the storage volume generated by HCA systems. The remaining storage comprises numerical results derived from images by analysis algorithms, and metadata or annotations, which are used to organize, search, and retrieve information. 1
Exploring the data mountain IN Cell Miner HCM Cellular Scientist Allows you to navigate through a project, from assay design to detail at the cellular level, allowing easy access, discovery and annotation of critical information Links image data to analysis results putting information into the context of an experiment, enabling identification of significant cellular events Provides a set of high-content data analysis and visualization tools to improve your scientific decisions Offers a secure environment and open standards to store, manage and annotate HCA data for collaborative research System Manager Builds on EMC Documentum platform, delivering a robust, scalable and enterprise-wide solution Uses Oracle database for performance and scalability Provides an advanced and intuitive system administration capability for information lifecycle management Offers a Web service SDK for application development and integration with external data sources Reduces total cost of ownership by using industry standards, Documentum, and Oracle and provides a centralized content/ system management 2
Streamlining the HCA data flow IN Cell Analyzer high-content systems automatically acquire high-quality images from cell-based assays. These images are then analyzed by IN Cell Investigator software, providing quantitative data for downstream analysis and decision making using Spotfire DecisionSite and other software tools. IN Cell Miner HCM is a client-server based content management solution that complements the IN Cell Analyzer instrument and IN Cell Investigator software. It streamlines the HCA data flow by providing a central repository for raw image data and numerical results, placing them into a searchable context. Stored data can be accessed via a feature-rich HCA-specific desktop client while the EMC Documentum content server application ensures reliability, scalability, and performance. The result is a system that can easily deal with the unprecedented amounts of data generated by HCA. Questions, data, and, materials (eg cells and compounds) Downstream processing and decision making Annotations Search Import/Export Project definitions IN Cell Miner HCM IN Cell Analyzer Image analysis IN Cell Investigator Data analysis Fig 2. IN Cell Miner HCM enables the storage, retrieval, and transfer of data across the IN Cell analysis platform. 3
Getting started Scientists interact with IN Cell Miner HCM through a rich, full-featured desktop client. The interface is tailored specifically to the HCA workflow and provides easy access to images, annotations, and numerical data. The IN Cell Miner HCM homepage (Fig 3) includes a ribbon bar at the top of the page that provides direct access to all projects, common queries, and key functions. This makes it easier for new users to get started while expert users have access to more advanced functions. From the homepage you can: Resume your work after your last session Import new data Access existing data through projects or queries IN Cell Miner HCM uses different Aspects to view and zoom into your data. In addition to the homepage there are Project, Plate, Well, and Cell Aspects, with each Aspect providing review tools appropriate to the level of data (Fig 4). Fig 3. The client performs the bulk of any data processing operations itself enabling a high level of performance and functionality. Fig 4. Well Aspect showing some key interface elements (clockwise from left): Guided Query bar for querying data sets; Ribbon bar for access to key functions; Context Viewer for viewing detailed properties, charts, and images; flexible data table for numerical results; and central data display for plate maps or thumbnail images. 4
Getting organized Data can be navigated using a multilevel hierarchy that reflects the project structure (Table 1). Such a hierarchy makes it easier to review related results when looking for promising candidates. Table 1. Project hierarchy The multilevel hierarchy within IN Cell Miner HCM allows you to create a screen containing all runs from a variety of assay types in one place. You can then search within your defined project and review images, charts, and component properties at the required level. Store different types of data including images, protocols, results, and annotations Manage data at project, screen, run and plate level Associate protocols, materials or compound list with the appropriate project levels Associate multiple image stacks with one plate Associate results from different analysis protocols with one set of images Level Project Screen Run Plate Well Key functions Holds all data belonging to one research project. Access rights are managed at this level. User-defined collection of multiple screens. User-defined collection of multiple runs. A screen might hold all data belonging to one aspect of the project. User-defined collection of multiple plates. A run might hold data form all plates read in one run of the instrument. The plate refers to the physical object that has been used for imaging. The plate has undergone some sort of treatment and holds specific samples. A plate can hold multiple image stacks (e.g., different time points, exposure times, and associated results). Physical location on plate, holds specific sample and treatment conditions (e.g., compounds and concentrations). Image stack A set of images acquired from one plate in one operation using the same acquisition protocol. Images have five possible dimensions: x, y, z, channel (wavelength), and time. Analysis results Numerical results derived from a specific image stack using the same analysis protocol. Fig 5. The IN Cell Miner HCM Project Aspect allows the user to set up and define the hierarchy of their projects. Shown here is a simple project (orange) with two screens (purple) and two runs (yellow) that hold five plates (blue). There are also corresponding acquisition protocols (pink and dark yellow). The navigation bar on the left allows easy navigation around large projects whereas the central Project Canvas provides a visual representation of the project. Properties of selected objects are displayed on the right-hand panel. 5
Annotating and analyzing data IN Cell Miner HCM stores data based on concepts pioneered by open-standard communities such as the OME (Open Microscopy Environment) and MIACA (Minimum Information About a Cellular Assay). Descriptions of experimental detail can be annotated to HCA data allowing assay results to be searched and placed into biological context. Rich annotations of assay conditions such as gene names and incubation temperatures allow searching for data in a variety of ways and increase the possibility of uncovering both expected and unexpected correlations. IN Cell Miner HCM uses a Guided Query bar for interactive data retrieval (Fig 6) and it is possible, for example, to query data based on the following. Plate, assay, or analysis names Hierarchy level Experimental conditions (e.g., compounds, reports, cell lines) Cell measures (e.g., cell number, nuclear size) Once data has been retrieved, it can be reviewed using table and graphing functions in the IN Cell Miner HCM or transferred for further visualization and analysis to applications such as IN Cell Investigator, Spotfire DecisionSite and Microsoft Excel. Fig 6. IN Cell Miner HCM provides the user with general HCA analysis tools, such as curve fitting, dose response calculations, Z, and signal-to-noise. Fig 7. The auto compare feature enables side-by-side comparisons of in-plate and cross-plate field with overlay information. Presentation can be automated across entire project. 6
Securing productivity IN Cell Miner HCM is a client-server application based on the EMC Documentum Content Server 5.3 OEM Edition and takes advantage of its proven architecture and advanced content management features. IN Cell Miner HCM provides: Controlled data access by defining security levels and user rights Life cycle management for project data Scalability from small workgroups to large enterprise IN Cell Miner HCM is Designed for Documentum accredited, a certification that signifies IN Cell Miner HCM: Meets the stringent quality levels expected for Documentum-based solutions. Follows best practices for design, development, deployment, and support to enable high productivity from out of the box. Employs Documentum services correctly and only utilizes supported interfaces to enable customers with existing Documentum installations to integrate IN Cell Miner HCM seamlessly with other missioncritical applications. IN Cell Miner HCM manages data ranging from workgroup environments to enterprise-wide applications. It supports a variety of storage systems ranging from direct attached RAID arrays and network attached storage devices to EMC CENTERA CAS content addressed storage suited for situations when regulatory compliance and data security are paramount. Fig 8. Securing productivity Open Standards based Comprehensive & Extensible Data model Enables seamless exchange of data Documentum Documentum infrastructure Robust, scalable & extensible IN Cell Miner Desktop & user experience IN Cell integration HCA expertise & ease of use 7
Supporting performance IN Cell Miner HCM is supported by the specialist IN Cell support team and can be supported remotely via Bio Insite. Bio InSite is a secure digital connection between GE Healthcare professionals and your system. It is an interactive help line to accelerate knowledge sharing and simplify troubleshooting so you can keep working smoothly. This easy-to-use technology utilizes a highly secure connection between GE Healthcare and your system. It is easy to implement and requires no modification to your IT network. With Bio InSite, you can focus on science, unlocking the full capability of your IN Cell Miner HCM installation, and boosting productivity in your laboratory. 8
Technical specifications PC specification Recommended specifications: Workstation class PC Intel Xeon (55xx series) processor with four logical cores or more (2.0 GHz or higher) 4 GB RAM 10 000 RPM or higher hard drives Windows XP operating system SP2 or higher (32-bit processor) Gigabit Ethernet adapter card Minimum requirements: Windows XP Professional operating system SP2 or Windows Vista (Professional or Enterprise) (32-bit processor) PC-compatible computer with a Pentium 4 processor High-resolution graphics display (1024 x 768 x 24 bits); two monitors recommended 1 GB RAM 1024 MB Paging file Gigabit network adapter 15 GB free disk space on the installation hard drive Server specifications Recommended specifications: Server class hardware Intel Xeon (55xx series) processor with four logical cores or more (2.0 GHz or higher) 4 GB RAM 10 000 RPM or higher hard drives configured in RAID-5 configuration Windows Server 2003 R2 with SP2 (32-bit processor) Gigabit Ethernet adapter card Modular smart array of drives with an expandable storage capacity (minimum 1 TB) Provision of host bus adapter card for the external storage connectivity such as a tape backup drive for archive Minimum requirements: Windows Server 2003 R2 with SP2 (32-bit processor) Oracle 10g Release 2 (10.2.0.4)/ Oracle 11g Release 1 (11.1.0.7.0) Server-grade computer with dual core 2.3 GHz processor 4 GB RAM 15 GB free disk space on the installation hard drive Gigabit network 1 TB RAID storage device Ordering information For additional product information or to request a quotation, please contact your GE Healthcare Sales Specialist. 9
For local office contact information, visit www.gelifesciences.com/contact www.gelifesciences.com/incell GE Healthcare Bio-Sciences AB Björkgatan 30 SE-751 84 Uppsala Sweden GE, imagination at work, and GE monogram are trademarks of General Electric Company. Bio Insite is a trademark of GE Healthcare companies. EMC and Documentum are trademarks owned by EMC Corporation, Spotfire and DecisionSite are trademarks owned by Spotfire, Inc., Intel, Pentium, and Xeon are trademarks owned by Intel Corporation, Microsoft, Excel, and Windows are trademarks owned by Microsoft Corporation, Oracle is a trademark owned by Oracle Corporation. 2008-2011 General Electric Company All rights reserved. First published July 2008 GE Healthcare Bio-Sciences Corp, 800 Centennial Avenue, P.O. Box 1327, Piscataway, NJ 08855-1327, USA GE Healthcare UK Ltd, Amersham Place, Little Chalfont, Buckinghamshire HP7 9NA UK GE Healthcare Europe GmbH, Munzinger Strasse 5,D-79111 Freiburg, Germany GE Healthcare Japan Corporation, Sanken Bldg., 3-25-1, Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan 28-9357-35 AC 08/2011