Keeping Workflows Moving – Data Management for Microscopy

Data Management System

Stream

BE IN COMMAND OF YOUR DATAControl workflowsManaging a workflow and the resultant data is all about being in control of every aspect. Solutions that help administer and integrate the components will therefore improve the overall workflow and can significantly increase efficiency. The Olympus ‘Stream’ Client/Server Data Management System combines all the tools needed for users to control, collect, calculate and communicate their work with the ease of a flexible and highly intuitive interface.

Data Management 4–7More is required in less time at a lower cost, but achieving this is a challenge in itself. Olympus Stream takes the strain out of this requirement by putting you back in control of your data and therefore makes workflows flow!

Straight to the Result 8 –13From before you start and until after you finish, Stream will manage the workflow requirements of any imaging based project leaving users to work on generating data and producing results.

Technology 14 –15Unique, novel, peerless… Stream brings the advantage of years of industrial imaging experience together with modern flexible programming to provide the only software system required for managing imaging project workflows and data.

Your Vision: Our FutureOlympus is dedicated to ensuring that the best solutions are available for your work, from microscopes and digital cameras to software and data storage. The Olympus Stream brings all of our experience to you, improving your workflow and data management. As a result, our goal is your success, both now and in the future.

2 CONTENTS

BE IN COMMAND OF YOUR DATA With a growing amount of data to manage, multiple users and the desire for greater data security, conventional Windows-based databases quickly become inadequate. Stream, Olympus’s client-server-based data management system developed especially for microscopy, ensures that even with large amounts of data and many users, workflows run efficiently and the greatest possible data security is provided.

Unlimited usersA By utilising careful architecture design and leading SQL systems, Stream avoids the common user-overload problems of conventional data storage systems. The client/server system leaves the data on the server and only downloads a file to the client computer if it is being viewed or edited. Therefore, access is unlimited even when there are a maximum number of users online.

Unlimited Data CapacityB Stream has the capacity to manage an unlimited amount of data and utilises the database management facilities of either Microsoft SQL or Oracle Server. Both ver-sions therefore offer excellent bandwidth for high volume data access.

Fast Data AccessC Data can take the form of images, analysis results, text and voice comments as well as supporting information such as order codes and tracking numbers. This is why storage solutions need to offer more than just the storage capacity. They also need to be carefully structured for fast navigation and retrieval. With Stream, data are organised in a system hierarchy under the relevant project, job or order. Extensive search functions and pre-defined search masks guarantee the fastest possible access to the data needed all the time.

Security/Access RightsD In some cases, the security of data is not only important but essential and there-fore Stream has a number of solutions to provide watertight protection. Access to a project or to individual project data can be restricted to a group or to individual users. Stream offers standard authentication via SQL log-on with user name and password. Stream can be integrated with the Active Directory and LDAP (Lightweight Directory Access Protocol) meaning that it will accept the user’s windows logon for single sign-on (SSO) access. Secure File RepositoryFor the ultimate security, an optional Secure File Repository can be established which ensures that files are only visible to users with permission to access them and only when they are using Stream, therefore there is no way for unauthorised users to know that the files exist – even if they are using Windows Explorer.

DATA MANAgEMENTAnything but conventionalIn designing Stream, Olympus realised that it had to provide something unique, something that would really make a difference to users. Olympus therefore looked very closely at the entire work-flow in industrial laboratories and designed a highly versatile data management system with the added benefit of hardware control, image collection and analysis, as well as an exclusive report composer.

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A Unlimited number of usersLarge labs and entire companies can use data jointly

C Fast data accessWith extensive search functions

B Unlimited data capacity And excellent bandwidths for data access

D Extremely high data securityFiles are only visible to users with the appropriate access rights.

LIMSC Stream can exchange information with LIMS (laboratory information manage-ment software) as well as ERP (Enterprise Resource Planning) and CRM (Customer Relationship Management) systems, Existing data, such as order numbers and relat-ed customer data, is available at every Stream workstation and can be automatically inserted into reports, for example.

ImportD Images, including associated meta-data (such as magnification, exposure time etc), can be imported from any image source such as electron microscopes and cameras.

InterfaceStream has been developed with interfaces to digital communication protocols such as COM (Component Object Model) and ODBC (Open Data Base Connectivity), which enable easier interfacing with other programmes.

Taking advantages of possibilitiesOlympus has produced a number of software solutions for materials analysis. Stream’s capabilities can be extended by adding the advanced analytical program-mes from the Olympus analysis family and integration with any existing A4i data source.

Olympus analysisE Stream is fully compatible with the peerless Olympus analysis analytical software packages making even complex particle analyses easy to do – either directly within analySIS or within Stream, using easy-to-program macros. a4iStream can work with databases from existing a4i Docu installations and therefore there is no need to import the data for read-only requirements (Full access is avail-able if the data is imported).

From the smallest to the largestF No matter which size of laboratory or enterprise at which ever level, Stream offers a new standard in client/server image data management, for control, collection, cal-culation and communication.

Workgroup EditionOlympus Stream Workgroup Edition is ideal for smaller workgroups and enables simultaneous log-on for up to 5 users based on Microsoft SQL Server 2005 Express.

Enterprise EditionThe Stream Enterprise Edition is a professional solution for enterprise data manage-ment. It handles an unlimited number of users, assignment of user rights, integration with LIMS and ERP and at the same time expands the possibilities removing all lim-its to workflow productivity and efficiency in the modern lab. The Enterprise Edition supports Microsoft SQL and Oracle Server.

UNLIMITED VERSATILITYData storage is only one requirement of an imaging and analysis process. The actual control of the hardware and acquisition of images are the first processes in any system; Stream integrates these seamlessly.

Image data management from the startIntelligent data storage is only one of many requirements for digital image acquisition and analysis. This is why Stream supports the workflows right from the start with effective microscope and camera control.

Microscope ControlA B Stream has built in control capabilities for Olympus’s extensive range of micro-scopes, allowing users to set magnifications, change observation methods control motorised stages and store all the relevant settings. Stream can also be used for controlling other light and electron microscopes as well as industrial endoscopes. Camera ControlThe most important data to Stream users are images. Stream allows control of both digital microscope cameras (such as the Olympus DP71) and digital photograph cameras (such as the Olympus E-Series). Stream can be used to set exposure times, real–time shading correction, white balance and actually record the image.

Efficient integration of existing data sourcesC Stream is designed to integrate with existing data sources on a network. It can import images and uses standard interface protocols to communicate with other software programmes.

Acquisition of metallic microstructure using light microscopy

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Acquisition of metal fracture microstruc ‑ ture using scanning electron microscopy

Particle analysis and classification

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Image properties, microscope and camera settings are saved with each image

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START WITh A gOOD STRUCTUREA Whether you wish to continue working on a particular project or begin a new project, Olympus Stream helps you structure the work efficiently right from the start.

Using existing data sources efficientlyB Pre-existing information such as customer data, delivery dates from LIMS or order processing systems can be used to initiate a project. This minimises the need to re-enter the same data, thus increasing data consistency. By the same token, the information on printed routing slips can be reduced to the essentials – such as just the order number. Ideally, this can be condensed into a bar code or a transponder on the sample.

Custom-tailored data entryB Data entry can also be configured for a specific task, for example, categorising samples according to specific characteristics. This entry process can be standard-ised according to user-defined data-entry masks and drop-down lists. This makes order entry significantly more efficient and ensures that the file storage structure is well-organised.

Not seeking – findingC It is often helpful to be able to reference existing results in order to compare a fracture image from a current damage case with similar past cases. The organisa-tional structure and the extensive search and filter options of Stream ensure that all relevant data is located quickly without any tedious folder searches.

STRAIghT TO ThE RESULTFastest route to successFor workflows where image acquisition plays a major role, individual data sources such as imag-es, text, analytical results, and diagrams, can number into the thousands. Storing and maintaining traceability on each of these becomes extremely difficult. Olympus Stream helps you not only to keep things clearly structured, but also controls all important processes ranging from image acquisition to the finished report leaving the users free to do their jobs. As a result, workflows become much easier to manage, more efficient and quicker.

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Stream database structure

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Sample data entry mask

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Project list view

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gETTINg ThE PERFECT IMAgEStream does not simply structure your data professionally, it also controls all important devices such as cameras and motorized stages necessary for per-fect microscope acquisition.

Everything under controlA With Stream there automated microscope components, and camera can all be controlled from within Stream in real-time. All of the settings are available allowing the user to set, exposure times, focus the image, change objectives, and apply-ing colour and shading corrections. The digital zoom – operated with the mouse wheel – enables users to quickly check the live image window to be sure the de sired details are actually captured by the camera – before actually acquiring and saving the image.

Advancing PhysicsB C Stream also makes it possible to transcend the limited depth of focus of high-resolution microscopy through Extended Focal Imaging (EFI). A sample with a depth too great for a single focal plane can be imaged clearly by combining the in-focus elements of a Z-series of images.

Capture more informationD An image is only as good as the information you can gain from it and therefore Stream ensures that you capture more than just pixels. Real-time sharpness control ensures that your image yields maximum detail fidelity – reproducibly and independ-ent of the user. Stream automatically records image parameters such as exposure, X/Y calibration and objective used. A scale bar at the edge of the image provides information on the actual dimensions.

MEASURE ITImage acquisition is usually just a means to an end. The quantitative results are what really count – such as a basic two-dimensional length measurement as well as more complex multi-phase particle analyses. Stream ensures that results are available faster, are reproducible and are saved securely.

Measuring in live imagesE Because cameras can be controlled by Stream and images automatically scaled, measuring can be done within the live image directly. An existing acquisition can be superimposed on the live image to enable careful comparison and consistency.

2-dimensional measurement F The user can access the most frequently used measurement functions directly via the self-explanatory buttons on the user interface. Measurement values are displayed automatically on the image itself and in a sheet. Furthermore, an extended menu provides definitions for the measurement parameters such as mean, maximum or minimum diameter.

Automated material analysisFor some images or even entire projects, more measurement functions are required. Stream interfaces with Olympus’s advanced analySIS software tools directly within the Stream user interface and results are automatically appended to the Stream project folder.

The Personal Touchg h Sometimes a little extra explanation is needed to help describe a feature or simple to comment on an image. Stream enables users to add overlays such as text annotations, simple drawing marks or even audio comments.

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Setting parameters for generating images at an extended depth of focus

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Image without (left) and with (right) opti‑mised depth of focus

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Real‑time sharpness display

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Selection and definition of the measure‑ment parameters

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Recording a voice message

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Formatting a label

Right: Stream acquisition screen with live image, camera and microscope control

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Left: Stream editing screen with direct access to measurement functions

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REPORTINg IS DONEWhen all is said and done, the project needs to be put into a report format for the customer – be they internal or external. Stream is an essential interface between all the elements of the project workflow from conception through to completion. The report composer is a completely new concept and is the perfect solution for creating consistent and coherent reports - as simple as A-B-C.

Firstly - Select templateA Templates make maintaining consistency extremely easy, they define the way in which data are displayed and do this the same every time. Any number of templates can be used to compose a report. A title page is defined containing certain standard information such as order number, processing personnel and a detail zoom of the component investigated. This is followed by the page templates for displaying imag-es and individual results. Page templates define the number and size of images to appear on the page along with the scale and image information (eg, exposure time) to be shown in the image description. In addition, a placeholder for the detail zoom can be defined.

Secondly - Add dataOnce the report instruction is defined, specifying the templates to be used and their order, any number of images and data from the database can be added via drag and drop. Stream calculates the number of report pages needed automatically. The order of templates and data can be changed anytime directly in the report instruction file (termed ‘report recipe’). Stream handles the information related to the images such as scale and magnification, and automatically adjusts image orientation and size based on standard settings.

Done - generate reportB Once all the templates and images are in the correct order, the user simply has to click on the report generation button and the report appears onscreen. The report is generated using the saved report instructions (report recipe) as well as associated data. The user can scroll through the pages of this report and adjust various aspects such as detail zooms.

Perfecting the reportC If any changes are needed such as more (or less) images or pages, an additional or different template or even just a change of data or page order, it is simple to switch back to the composer view, make the changes and generate the report again. This flexibility ensures that once created, a report can be edited without starting again.

ExportingD Due the versatility of the XML format, the report can be read by any XML inter - face or can be exported from Stream into Microsoft Word (.doc file) or Adobe Acrobat (.pdf file) formats for electronic or print distribution. Using the Microsoft Word format also enables the Stream report to be added to a larger overall report.

Communicating resultsE With reports accessible in a number of different formats and the original data available with all additional information, communication of project findings is possible via a number of methods. Stream users can access data and reports directly from the project database. Individual files can also be emailed, printed or ‘burnt’.

Status reporting to network systemsDue to Stream’s seamless integration with existing LIMS or ERP systems, the com-pletion of the project can be updated on these other systems allowing them to move the process onto the next stage.

A Report composerMakes generating professional reports simple

B Report generatorGenerates reports based on tem‑plates and user content

D Data exportTo Word and PDF

E Mail reports directlyVia e‑mail

C Finished report Reports can be modified at any time

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CONFIgURINg STREAM INDIVIDUALLY In order to guarantee the best Stream system configuration, Olympus can ana-lyse the existing infrastructure and determine the precise requirements of the end user. This is how Stream guarantees perfect integration with all company processes.

Software requirementsStream uses the excellent DBMS facilities of either Microsoft SQL Server 2005 (or SQL Server 2005 Express) or Oracle 9i/10g Server (or Oracle XE). The Stream Workgroup version is designed specifically to work with Microsoft SQL Server 2005 Express which offers the correct level of functionality for smaller groups. To be able to take full advantage of the Stream Enterprise Edition, the full DBMS version is recommended.

User rightsA B User rights are assigned under four default roles: Administrator, Power User, User and guest, which can all be modified for added flexibility.

Further to this, each project (or data record) can be assigned access rights to defined individuals or members of a group. Authentification is possible via SQL log-on when starting Stream or via integration with existing Active Directory and LDAP (Lightweight Directory Access Protocol) to provide SSO (Single Sign On) capabilities.

Secure file repository C To ensure maximum data security, Stream offers the optional Secure File Repository (SFR) module. As a extra layer of security, the SFR works with Stream to handle file requests based on a user’s access permissions and therefore users with-out permission to open a file will not even see it in their file directory. Unauthorized users thus have no chance to manipulation files.

IntegrationOlympus Stream can be set-up to interface directly with existing order management, LIMS, ERP and CRM systems. Further flexibility is available with build in interfaces to digital communication protocols such as COM (Component Object Model), and ODBC (Open Data Base Connectivity) which enable easier interfacing with other pro-grammes. API (Application Programming Interface) functionality has also been added to enable the use of Stream processes by other programmes.

Access to existing databasesExisting records from other databases can be imported into Stream with all the rel-evant data and meta-data properly organised for work using Stream. It is also pos-sible to utilise some existing data-sources, such as an 4i database, without importing them (read-only access).

TEChNOLOgYThe right tools for the jobBehind every great advance is the careful utilisation of experience and technology. Stream is such an advance, setting a new level in workflow productivity by bringing all the tools needed to any number of users through an easy to use and comprehensive interface.

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User accounts can be classified accord‑ing to 4 standard groups (Rolls)

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The manufacturer reserves the right to make technical modifications without prior notice.

Postfach 10 49 08, 20034 Hamburg, germany Wendenstraße 14–18, 20097 Hamburg, germanyPhone: +49 (0) 40 23 77 30, Fax: +49 (0) 40 2 37 73 46 47 E-Mail: microscopy@olympus-europa.com

database client-server database for archiving images client-server database for archiving images

and other documents and other documents

supported DBMS Microsoft SQL Server 2005 Express1 Microsoft SQL Server 2005 Express1

Microsoft SQL Server 20052

Oracle 10g Release 22

Oracle XE3

Other DMBS versions upon request

size of all database tables 4 gB (not including documents) unrestricted4

number of simultaneous database users 5 unrestricted4

document storage file system file system

Secure File Repository (optional)6

user administration /user access rights managing users / user groups

variable rights for access to images and other documents

SQL authentication

Windows authentication (Active Directory/LDAP integration)

Single Sign-On

Stream specifications

Data management Workgroup Edition Enterprise Edition

Interfaces and image import

Interface to Olympus analySIS image-analysis software This interface offers direct access to powerful image-analysis functions

Image import file formats: TIFF, JPg, BMP, PCD, EPS, PNg, etc.

Image types binary, 8-bit gray scale, 8-bit pseudo colour, 16-bit grey scale, true colour (24-bit RgB)

Image processing

Intensity optimise and equalise contrast, modify grey values, etc.

Changing bit depth 8/16 bits, colour 8/24 bits, binarise

Colour modification colour spaces: RgB, HIS, colour channel separation, white balance, pseudo colour palette definition

Filters with preview function sharpen, edge enhance, mean, median, Sobel, Roberts, NxN, low pass, rank, shading correction

Image geometry Resize, mirror, rotate

Panorama function Manual (interactive) panorama image generation based on single saved images/image series

Image labelling

Overlays Use text, arrows, etc. for labelling in image overlay (also for live images)

Voice annotations Use text and voice annotations stored with the images

Standard functions

Measurement

Interactive measuring point-to-point distances (arbitrary, perpendicular), angles, polylines, polygons, circles, rectangles, ellipses, etc.

Report functions

Report composer easy report generation via drag and drop

Report generation template-based report generator

export to RTF (Microsoft Word)

export to PDF

1 Microsoft SQL Server 2005 Express is a free-of-charge version of the Microsoft SQL Server 2005. Limitations: 4 gB database table space, only 1 gB RAM and 1 processor are supported.

2 DBMS server and client licenses are not included. 3 Oracle XE is a free-of-charge version of the Oracle 10g Release 2. Limitations of Oracle XE: 4 gB database table space, only 1 gB RAM and 1 processor are supported. 4 Depends on DBMS and possible hardware limitations of the server. 5 Not available for Workgroup Edition. 6 Optional for Enterprise Edition.

Basic functions

Camera interfaces5 FireWire IEE 1394, USB2, frame grabber, TWAIN

MovieCreator/AviRecorder5 generates movies from individual frames or directly from the live image

Special interfaces SEM/TEM Integration

Extended image acquisition

Automated panorama function5 generates panorama images (requires motorized stage)

Infinite automated depth of focus5 generates images with infinite depth of focus (requires motorized stage)

Device control

Olympus microscopes BX, IX, MX, SZX

Stages/focus drives controls XYZ stages

Image acquisition

Documentation