Digital Media Management for the Life Sciences and Pharma

Transcription

1 Digital Media Management for the Life Sciences and Pharma ims bio is a professional digital media management system with which you can acquire, process, store, display and present digital images, movies and documents. ims bio is a platform independent, Java based client/server architecture and supports Oracle and SQL Server. Integral functions of ims bio include a comprehensive LDAP linked group and user management, extensive access right management for data and user functions as well as a highly flexible workplace configuration concept. A modular function and licensing concept with a wide range of optional, application specific client and server functions allows you to configure individual workplaces tailored to the specific needs of your work environment. A web viewer with efficient search capabilities allows you to access and display data stored in your ims wherever you are. Links and direct interaction with Project (PMS) and Laboratory Information Systems (LIMS, SLIMS, ELN) provide comprehensive and consistent access to media and related meta data at the microscope, analysis and office workplaces.

2 System Components ims Client ims Client is a user interface that you can customize to suit it to your specific workflows. It features automated media acquisition, movie recording, the analysis and processing of images as well as the automated creation of Microsoft Word reports and PowerPoint presentations. ims Client runs as a Java application on Windows, Mac and Linux workstations. It represents the user interface for all interactive workflows. System administrators can define to which tools and data users or user groups are granted access by preconfiguring role and task specific workplaces for them. Media Manager is a file explorer like view that provides you with data access and ergonomic, web like search modes. A set of tools helps you manage your content intuitively. You can automate entire workflows with just one macro. ims Server ims Server is the central management component of the ims: It communicates wiith ims Clients, ims Publisher, the database system and the file storage system. ims Server also maintains the communication with remote LDAP user/group management systems, handles data imports and exports through its internal XML Control Interface and coordinates the communication of other ims Servers in a cluster. Configurable tasks control database synchronization, automated import and export as well as workflows. A built in license management manages the distribution of fixed and floating licenses to ims Clients and ims Publisher. ims Server is a Java application/service that runs on Windows and Linux server. Built as a consistent single application independent of any communication with 3 rd party application servers, it provides best performance for time critical tasks such as ims Client and database communication. Native database drivers for Oracle and SQL Server guarantee high compliance with established database system providers. 2 Digital Media Management for the Life Sciences and Pharma

3 System Components Multi Server Operation Several ims Servers can be operated as services on a single server or a virtual machine (VM). This is of importance in complex environments operating multiple license pools and access right groups or for simultaneous operation of test, consolidation and productive systems. Digital Media Management for the Life Sciences and Pharma 3

4 Image Acquisition Media Sources and System Solutions ims bio provides a most flexible solution for any lab environment in microscopy by supporting a wide variety of media sources for the acquisition of image contents and related meta data. Digital cameras, scanners, microscopes ims bio supports the following sources: Digital microscopy camera systems Digital cameras for micro photography (analog and high resolution) Scanners for negatives, slides and X ray films Light microscopes for transmitted and incident light, fluorescence imaging Confocal microscopes 2 photon microscopes Stereo microscopes Scanning electron microscopes Transmission microscopes Micro probes Micro tomography devices Imaging plates Acquisition In digital media management systems efficient and comprehensive acquisition of media contents and related meta data in daily routine environments are key issues. Specialized interfaces for device control and data exchange minimise user interaction. Various file formats and small to large file sizes of images, movies and meta data Data acquisition at one click Automated acquisition of large amounts of image and movie files Automatic calibration of acquired media data Look alike acquisition user interface for all source types Flexible file name generation based on project/experiment contents Automatic image processing at acquisition time (shading correction, histogram equalisation, white balance, panorama image assembly, HDR, etc.) Z stack image series acquisition for Multifocus and 3D visualisation Time lapse and movie recording, Mosaic, HDR, MultiFocus Import/export of file header data to/from database fields (IPTC, EXIF, etc.) Support of 30+ different 2D image file formats (TIF, JPG, JPG2000, etc.) Acquisition of 3D/4D datasets from confocal, 2 photon, SEM/TEM, 3D tomography devices and files, including meta data and calibration information 4 Digital Media Management for the Life Sciences and Pharma

5 Optional Modules for ims Client Imagic Source TWAIN Source Image Processing Movie Editor Annotation Measurement Word Report, PowerPoint presentation Supplier independent user interface for the control of all analog and digital image sources supported by ims bio Read out and re store of acquisition relevant device parameters Consistent operation for all devices Storable configurations All Leica DFC cameras Jenoptik cameras CT3, C3, C5, C14+ Selection of Zeiss AxioCam cameras All Y/C (S Video) image sources Acquisition from 3 rd party sources with device specific TWAIN driver Standard image processing functions Rotate, mirror, brightness/contrast/gamma, invert, histogram equalisation, image size, crop, snapshot, binarise, windowing (brightness/contrast setting in 16 bit images), white balance, shading correction, cloning Editor for MPEG 2 and MPEG 4 movie files Assembly of sub sequences Extraction of single images Annotation of images on overlay Line, rectangle, circle, textbox Individual configuration of annotation properties Visibility filters Export to Microsoft Word and PowerPoint Interactive measurements on overlay of images Distance, multiple distance, parallel distance, area, circle, angle, object counter Individual configuration of measurement properties Visibility filters Export to Microsoft Word and PowerPoint Automated creation of Microsoft Word reports and PowerPoint presentations on keystroke Image/field contents transfer directly from Media Manager or via presentation module Showcase User defined templates Digital Media Management for the Life Sciences and Pharma 5

6 From Image Acquisition to Perfect Presentation Creating presentations, publications and reports usually takes a lot of time. With the ims Showcase module and our Microsoft Office plug in you can create and edit Microsoft Word reports and PowerPoint presentations at one click. Documentation in Microsoft Word and PowerPoint Creation of reports and presentations at one click The ims Showcase module with its WYSIWYG interface allows the interactive creation of complete Word reports and PowerPoint presentations inside the ims application, based on individual layouts. Drag and drop media contents and meta data from the Media Manager to Word reports and PowerPoint presentations, or directly into your document AutoReport creates complete Word documents or PowerPoint presentations with image collections Zoom is a function to magnify details of images in Word reports or PowerPoint presentations, including magnification and calibration information The Image Editor allows processing of inserted images with basic functions The Trace feature finds inserted images in Word reports and PowerPoint presentations in the Media Manager and updates them in the office document Image Backups and Archive Extracts Easy to use image and project data backup and storage to CD or DVD Access to selected images and data for presentations on laptops using the Presentation Export feature 6 Digital Media Management for the Life Sciences and Pharma

7 Benefits Automation of complete image acquisition process, featuring project oriented file name generation, macro controlled image processing and centralized storage and calibration for all media objects acquired Automatic import of existing data structures and related media and meta data into the Media Manager Multi hierarchical Media Managers with customer defined folder/field structures Individual Workplaces with predefined function and data access support rolebased work flows. Intuitive, file explorer like display of hierarchical database structures display media data in overview lists, image galleries and editable forms Flexible and fast data query with Internet like did you mean spell checking for all meta data contents Ultra fast query response due to highly indexed data management Individual, named media data collections for fast reporting, presentation, export, publication Internal media data viewer with editor capabilities allows interactive measurement and annotation, image processing and movie editing User defined hierarchical keyword catalogues for simplified field entry and consistent data management, supporting synonyms and list import General support for all types of documents, special integration of Microsoft Office Word, PowerPoint and Adobe PDF documents Import of document contents into Media Manager text field allows contentbased queries for media objects Edition of acquired media objects in assigned application on a key stroke, with overwrite or new storage feature in Media Manager Support for most established image file formats in microscopy, such as Leica Multiple TIFF, Zeiss CLSM and ZVI, Olympus multiple TIFF, Biorad Pic, Metamorph STK, Bitplane IMARIS IMS, Gatan DM2/3, JEOL TIFF, OME and many more User defined server tasks for automated import or export of media data, synchronisation between external and central databases, transfer of productive database contents to science/teaching/presentation databases, etc. Export of media objects in open XML format for compliance with 3 rd party LIMS and project management systems Web browser for installation free search, view and download capabilities to all media object data from any internet connection, with identical user data access and function rights as with client application Automated and customized workflows Fast and flexible data access Integrated work environment Digital Media Management for the Life Sciences and Pharma 7

8 Technical Highlights High system scalability from stand alone single clients up to enterprise media management solutions Platform independent Java clients for Windows, Mac and Linux environments Platform independent Java server for Windows or Unix/Linux server environments Data storage in established and open Microsoft SQL Server or Oracle database formats Unique supplier independent user interface for all analogue and digital image sources Reading 60+ light and electron microscopy data formats with related meta data Link to lab based imaging systems, such as Gel/Blot scanners Installation free LAN, intranet and internet access to media and related meta data for searching, viewing and downloading with ims Publisher LDAP support for centralised group and user management Generic XML control interface for communication and data exchange with external applications (LIMS, ELN, PMS etc.) 8 Digital Media Management for the Life Sciences and Pharma

9 Optional Modules for ims Server Signature Scheduler Oracle XML Import XML Export Stores signature code of original document in Media Manager User function for status display: original/not original Time controlled ims Server tasks Multiple tasks per ims Server Defined intervals with single minute resolution Support for Oracle versions 9i, 10g, 11g Reads XML file from pre defined path Creates/updates archive entries with field data and images/documents Documentation and example code Creates XML file in target path Copies field data and images/documents Event and content controlled activation of export HL7 Import HL7 version: 2.5 Supported messages: A01, A02, A03, A04, A05, A06, A07, A08, A09, A10, A11, A12, A13, A14, A18, A23, A32, A33, A34, A38, A40, A42, A50 HL7 Export HL7 version: 2.5 Supported messages: ORU R01 DICOM PACS Archiving LDAP Import XML User Administration Time and event controlled export of images and patient oriented meta data in DICOM format to PACS Transfer protocol guarantees correct transfer Re import into ims Archive via PACS Query/Retrieve User authentication via online user/password request to LDAP User import and update into ims system management Support of LDAP nested membership Support of MS Active Directory (AD) Substitute for LDAP user management based on XML imports Digital Media Management for the Life Sciences and Pharma 9

10 Optional Modules for ims Server Imagic Bildverarbeitung AG Europastrasse 27 CH 8152 Glattbrugg Tel: XML Control Interface Watermarking Remote Sync Offline Acquisition Dongle Protected License Server Clustering AETitle DICOM Import Bi directional XML data exchange between external application and ims Proxy service Control of ims Client functions Data exchange with ims Server Activation of ims Publisher User defined image or text watermarks for large thumbnail image Transparency and size selectable Unidirectional synchronisation of remote SQL Server/Oracle archives into central SQL Server and Oracle archive Time and event controlled execution Client log in and acquisition without server connection Storage of acquired documents and meta data as local XML files Manual or automatic copy of locally stored files into image archive on next network log in USB Stick for mobile ims Server license usage Multiple ims Servers on different application servers with identical database access DICOM image import from modalities into image archive or via DICOM router into ims Client Image and meta data extraction with optional JPG conversion and storage in image archive Time and event controlled conversion of archived image and meta data to DICOM format, export to PACS, automatic re import from PACS into image archive Imagic (UK) Ltd Woodborough Pewsey Wiltshire SN9 5PF Tel: Fax: uk.com uk.com Images on pages 1 and 2 kindly supplied by: Syngenta and EMEZ ETHZ, ZMB UNIZH and EMZ UNIL ( 2012)

11 Technical Specification ims Client Programming language Java 1.6 Communication protocol Supported operating systems Microsoft Word and PowerPoint modules Camera and microscope drivers, TWAIN sources Installation Configuration TCP/IP (addresses and ports to ims Servers) Windows (XP, Vista, Windows 7), Linux, Mac OS X Windows (XP, Vista, Windows 7) Windows (XP, Vista, Windows 7) Small loader application copied to client path. Auto update without admin interaction Copy of full ims Client application to Client path. No auto update (e.g. Citrix environment) No system configuration for client installation. Pre configured Workplaces are started with user login ims Publisher Programming language Java 1.6 Web server Servlet Engine Tomcat 6.0 (integrated standard installation) Apache2 Tomcat 6.0 (integrated standard installation) Glassfish Supported operating systems Windows Server 2003, Server 2008, Vista, XP, Windows 7, Unix (requires Java 1.6) Linux Communication protocol Installation Configuration User Management HTTP or HTTPS with port. Installed firewalls have to unlock protocol and port. Copy to server path. A WAR file is copied to the installed servlet engine. Browser based configuration wizard for all ims Publisher settings User name/password log in with authentication on ims Server

12 Technical Specification ims Server Programming Language Java 1.6 Supported Database Systems Communication Protocol Supported Operating Systems Licensing Memory Requirements Installation Configuration System Check User Management Failover security Load distribution Task Management SQL Server 2005/2008 Optional: Oracle 9i, 10g, 11g The ims Client to Server communication is TCP/IP based and requires a customerdefined IP address and port. The communication protocol is RMI. A firewall between ims Client and ims Server firewall has to unlock this IP address/port and protocol. The connection may be secured by SSL encryption. Windows Server 2003, Server 2008, Vista, XP, Windows 7 Unix (requires Java 1.6) Linux (requires Java 1.6) XML File License pool for distributed, concurrent user log in Group assignment at module level Optional assignment of licenses to workstations Min. 4 GB on database server Copy to server path Configuration wizard for all system settings Web based system monitor Manually, or LDAP system with the following functions: Automatic import of users from LDAP to ims User Management User password authentication for ims Client and ims Publisher Log in distribution to multiple servers (server clustering) Automatic Load Distribution onto multiple ims Servers (server clustering) Multiple separated time or event controlled tasks for data import, export and synchronisation