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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.
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Exploring the data mountain
IN Cell Miner HCM
Cellular Scientist
System Manager
• 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
• Builds on EMC Documentum platform, delivering
a robust, scalable and enterprise-wide solution
• 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
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• 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
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
Image analysis
IN Cell Analyzer
Data analysis
IN Cell Investigator
Fig 2. IN Cell Miner HCM enables the storage, retrieval, and transfer of data across the IN Cell analysis platform.
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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.
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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.
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.
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
Table 1. Project hierarchy
Level
Key functions
Project
Holds all data belonging to one research project.
Access rights are managed at this level.
User-defined collection of multiple screens.
Screen
User-defined collection of multiple runs.
A screen might hold all data belonging to
one aspect of the project.
Run
User-defined collection of multiple plates.
A run might hold data form all plates read in
one run of the instrument.
Plate
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).
Well
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.
• Associate results from different analysis protocols
with one set of images
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.
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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.
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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.
Securing productivity
IN Cell Miner HCM is a client-server application
IN Cell Miner HCM is “Designed
based on the EMC Documentum Content
for Documentum” accredited,
Server 5.3 OEM Edition and takes advantage a certification that signifies IN Cell Miner HCM:
of its proven architecture and advanced
• Meets the stringent quality levels expected for
content management features.
Documentum-based solutions.
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
• 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
• Comprehensive & Extensible Data model
Open • Enables seamless exchange of data
Standards
based
Documentum
• Documentum infrastructure
• Robust, scalable & extensible
IN Cell Miner
• Desktop & user experience
• IN Cell integration
• HCA expertise & ease of use
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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.
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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.
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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