The OMERO Platform An open source solution for microscopy metadata management, visualization and analysis

C. Allan, C. Blackburn, J.-M. Burel, K. Eliceiri, P. Forbes, X. Jiang, M. Linkert, B. Loranger, S. Loynton, C. Macaulay, D. MacDonald, J. Moore, W. Moore, C. Neves, A. J. Patterson, C. Rueden, D. Sloan, A. Tarkowska, J.R. Swedlow OMERO Installs Oct 2008  Wellcome Trust Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK  Glencoe Software , Inc. S OMERO.server N OMERO.insight  Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, USA  Usable Image, School of Computing, University of Dundee, Dundee, Scotland, UK M OMERO.importer E OMERO.editor open microscopy environment

Recently, we have started adding in speci c image processing and analy- Manage Abstract sis functions, along with facilities for running your own self-scripted algo- OMERO.importer OMERO.insight Rate LOCI Bio-Formats rithms and transformations. View Bio-Formats is a standalone Java library for reading and writing micro- The OMERO Platform aims to provide a complete solution for image data OMERO is an open source development project and we welcome input, OMERO.importer is a desktop tool for importing over 30 dierent le for- OMERO.insight is a desktop tool for accessing, manipulating, collaborating, Measure scopy le formats. It is capable of parsing both pixels and metadata management. Both cross-platform and cross-language, OMERO provides advice, comments, and help. Go to http://www.openmicroscopy.org and mats into our centralized OMERO server. Designed as a re and forget appli- viewing and performing basic measurement on data stored in an installa- Attach for a large number of formats, as well as writing to several formats. highly-scalable remote access to your raw data and metadata from any- see what we are up to! cation, it is ideally suited for importing your images in the background, tion of OMERO.server. Search where in the world, even over a wireless connection. while you work, or operating after hours while your computer sits idle. The Data Management Tag Collaborate Bio-Formats's primary purpose is to convert proprietary microscopy importer's import queue enables you to browse and select les for import, • In the left-hand pane is a traditional tree-based view of the data hierar- Annotate data into the OME data model, an open standard. This may be stored organize them into projects and datasets, provide brief annotations, and chies in your OMERO.server. google: OMERO http://www.openmicroscopy.org/ as either OME-XML or the more space efficient OME-TIFF file format. organize them before import. Images can also be archived alongside • In the middle pane is a working area used to select and filter data to The Bio-Formats manifesto provides a thorough explanation and the import process, allowing you to retrieve your untouched image les work on. rationale of the directions taken while creating this library. from the OMERO.server at a later date, and the client's history feature • In the right-hand pane is a tool to work on the selection i.e. rate, tag, allows you to search and review your previous import sessions and then annotate, etc. re-import your images if desired. Viewing Bene ts For Users: • Allows visualization of 5D images (space, channel, time). There are several software packages that can use Bio-Formats to read Written using Sun Microsystems' Java language, OMERO.importer is cross- • Makes use of the OMERO.server’s Rendering Engine. and write microscopy formats. These include ImageJ, VisBio, OME, OMERO.server also provides a simple to use Google-style search interface platform compatible with all major operating systems, easy to set up, and OMERO.server for quickly finding data in addition to a more complete SQL-like language • Provides high-performance viewing of multidimensional images on VisAD, Endrov and MATLAB. simple to understand. It is built on recognized and robust technologies standard workstations, without requiring installation of high-powered for building reports and other data mining. and makes use of the Bio-Formats imaging package. Bene ts For Application Developers: OMERO.server combines enterprise database, search, scripting, security, graphics cards. Bio-Formats provides a library to support working with a large and interface technologies and serves as the foundation of our image Bene ts For Users: Measurement In addition, the server provides exible security mechanisms similar to a number of formats in there own software. The Bio-Formats library data management solution. Together these tools form a highly-scalable, • Easy to set up – one download provides you with a working importer • Draw Regions Of Interest (ROI) on the image: Squares, Ellipses, Polygons, Unix operating system, both in terms of users and groups as well as file provides a common interface to the developer regardless of le cross-platform, cross-language service for remote users allowing them on any platform compatible with Java 1.5. Lines. and directory permissions. format. As the library is improved and new formats added the devel- secure access to images and metadata from any internet connection. • Cross-platform – ideally suited for real world environments with multi- • Creates ROIs across Time and Z-sections. oper can take advantage of these improvements with little eort. Whatever your data dimensions – countless frames, high-resolution ple operating systems and system specs. • Measures the geometry and intensity values of the pixels under the ROI. In the latest release, support has also been added for sending self-scripted • Fire & forget operation – the importer’s queue • Views histogram of the intensity values under the ROI. images, or extensive videos – OMERO.server provides mechanisms for Bio-Formats is open source software licensed under the GNU General algorithms and transformations to where the data is stored rather than function lets you set up your import and then • Exports all results to a spreadsheet. managing your data and discovering new scienti c insights. Public License. bringing the data to you, again making the most of your data and time. continue with your day. Server Features • Robust le format support – over thirty dier- Display of Plates of HCS data, shown below, is currently in testing and we • Hibernate Query Language – All data in the server is queryable via HQL. ent formats supports and still growing! hope to include it in the next major release. Simpler than SQL, HQL provides powerful mining capabilities while free- Bene ts For System Administration: Digital ing the developer from low-level details like security and individual eld LEGEND loading. • Based on robust, open-source tools. Image Metadata Raw Metadata

Metadata e Acquisition Data Metadata • Stateful Services – In addition to storing data in the database, the • Ease of operation and cross-platform nature ta System server can remember settings and given state over the course of multi- means less training and technical support issues. y els esen c etad a penness r ple sessions. • Ideal for use “at the work station” – where image data is collected. i x M O P Utili t Quantitative # Format Extensions P Analysis • Row-level Security – Each entry in the database is protected by both a READ and WRITE flag for USER, GROUP, and OTHER. 1. Adobe Photoshop PSD .psd • Audit Trail – All interactions with the server are recorded in “Events” 2. Alicona 3D .al3d which can be examined by the system administrator. 3. Amersham Biosciences GEL .gel • Database Versioning – Each version of the OMERO database comes 4. Andor Bio-Imaging Division (ABD) TIFF .tif with all necessary upgrade scripts for safely moving your data from OMERO.server previous supported versions. 5. Animated PNG .png 6. Aperio SVS TIFF .svs Support is also provided for: Data Management, 7. AVI (Audio Video Interleave) .avi • Structured Annotations – Attach your own data to objects in OMERO Written using Sun Microsystems’ Java language, OMERO.insight is cross- Tagging, 8. Becker & Hickl SPCImage .sdt Querying • Scripting – Tools for running custom analysis and integration with platform compatible with all major operating systems, easy to set up, and CellProfiler simple to understand. It is built on recognized and robust technologies 9. Bio-Rad PIC .pic such as JHotdraw, a drawing library and the JBoss transactional framework. 10. Bitplane Imaris .ims Processed Metadata Metadata Visualisation Metadata Data Metadata It was built in collaboration with OME’s design ethnography team Usable 11. BMP (Windows Bitmap) .bmp Image. 12. DeltaVision .dv, .r3d google: OMERO.server http://www.openmicroscopy.org/info/OMERO.server Bene ts For Users: 13. DICOM .dcm, .dicom • Easy to set up – one download provides you with a working importer on any platform compatible with Java 1.5. 14. EPS (Encapsulated PostScript) .eps • Cross-platform – ideally suited for real world environments with multi- 15. Evotec Flex ple operating systems and system specs. 16. FEI .img • Remote access – manipulate, view data without sitting at the worksta- google: OMERO.importer http://www.openmicroscopy.org/info/OMERO.importer 17. FITS (Flexible Image Transport System) tions e.g. from your oce, in the lab, or your favourite internet cafe. OME Data Model OMERO.web 18. Gatan Digital Micrograph .dm3 Bene ts For System Administration: 19. GIF (Graphics Interchange Format) .gif • Based on robust, open-source tools. The OME Data Model was devised to allow the interchange of microscope OMERO.web client is a rich internet application that allows for the manage- • Ease of operation and cross-platform nature means less training and 20. Hamamatsu Aquacosmos NAF .naf data. It is an open standard providing a rich description of image metadata. OME Software Downloads ment, viewing, attachment, and association of les to images, datasets, technical support issues. 21. ICS (Image Cytometry Standard) .ics and projects. This includes a fully multidimensional image viewer running Information contained within the model can include: OME top level inside your web browser. Searching and tagging of information are avail- 200 22. Image-Pro Sequence .seq google: OMERO.insight http://www.openmicroscopy.org/info/OMERO.insight • Information about the Experiment itself Project able to further organise and manage data. 180 OMERO.server 23. Image-Pro Workspace .ipw OMERO.clients • Who is conducting the work 160 24. Improvision Openlab LIFF OME Server • What group the work is for Dataset The application provides a platform to further allow for collaboration be- 140 25. Improvision Openlab Raw .raw • A project and dataset structure to organize data tween individual scientists, groups or labs and a pathway for publishing 120 26. Improvision TIFF .tif • Detailed instrument and light path information Experiment work. It is specifically designed as a “thin” client, for remote access. 100 80 27. InCell 1000 .xdce, .tif • Light sources Downloads OMERO.editor makes it easier to describe the data associated with an Plate OMERO.web uses Django, a high-level Python web framework, jQuery, a • Filters 60 OMERO.editor experiment and then capture it in a structured and reusable form. 28. IPLab .ipl • Dichroic Mirrors new JavaScript library and Ajax interaction technology, to communicate 40 Screen with OMERO.server. It is a web application, that has the features and func- 29. JPEG .jpg • Objectives 20 OMERO.editor key features tionality of traditional desktop applications and transfers the processing OMERO.editor is an editing tool for scientists to record and manage their 30. JPEG 2000 .jp2 • Detectors 0 • Easier re-use of protocols by separating out the experimental variables. Experimenter experimental metadata. This tool is a stand-alone cross-platform applica- necessary for the user interface to the web client but keeps the bulk of Mar- Apr- May- Jun- Jul- Aug- Sep- Oct- Nov- Dec- Jan- Feb- Mar- Apr- May- Jun- Jul- Aug- Sep- • Import multiple small protocols (e.g. siRNAi treatment, Fix-stain) into a 31. Khoros VIFF (Visualization Image File Format) Bitmap .xv • Any associated OTF (optical transfer function) 07 07 07 07 07 07 07 07 07 07 08 08 08 08 08 08 08 08 08 the intensive data processing back on the application server. tion that saves les as XML documents. OMERO.insight can attach these larger protocol, to describe a complete experiment. • A powerful image object to work with representing Month 32. Leica LAS AF LIF (Leica Image File Format) .lif Group les to images and can also open OMERO.editor les attached to images. • Use Date-Time fields to schedule future experiments, and set pop-up • The environment of the sample For users the key bene ts are: reminders. 33. Leica LCS LEI .lei, .tif • How the sample is being manipulated Instrument Experimental metadata is represented within OMERO.editor in the form • No Installation Required – The client runs through the web browser • Future and past protocols can be browsed via Date-Time using the cal- 34. Li-Cor L2D .l2d, .tif, .scn • An unlimited number of channels of elds, which can be arranged hierarchically. A number of elds can so delivery of the application is instant, and can be used from any com- endar. 35. LIM (Laboratory Imaging/Nikon) .lim • Stage position on a per plane basis for tiling Image be used to describe a protocol or data model, by editing the eld name puter with an internet connection. • Search your OMERO.editor files using either a Key-Word search or • A 5-D structure (X, Y, Z, Channel and Time) 36. MetaMorph 7.5 TIFF and adding a description to each eld. In addition, a eld may be used to More-Like-This search to nd les similar to the currently viewed le. SemanticTypeDefinitions • A Screening model that supports multiple screens, record an experimental variable, or frequently changing parameter, such • Lock chosen fields to prevent editing, or lock only the protocol tem- 37. MetaMorph Stack (STK) .stk plates, wells and images with their associated rea- as a name, number or date. plate to allow editing of experimental variables. 38. Manager .tif, .txt gents. AnalysisModuleLibrary 39. MINC MRI .mnc The data model is provided as an XML Schema. This CustomAttributes • Instant Updates & Upgrades – New versions are automatically avail- 40. MNG (Multiple-image Network Graphics) .mng allows the creation of XML les to hold your data. This is able independent of operating system. the OME-XML format that has the raw pixel data directly 41. MRC (Medical Research Council) .mrc StructuredAnnotation • Rich set of functions – Including Drag and Drop data management, Manage Annotate encode into the XML. and a fully functional 5-Dimensional data viewer. 42. NEF (Nikon Electronic Format) .nef, .tif 43. Nikon NIS -Elements ND2 .nd2 We also provide a method of combining the OME Data Model with that View History For system administration the key bene ts are: imaging staple, the TIFF file. The OME-TIFF format allows the metadata to 44. nrrd (Nearly Raw Raster Data) .nrrd • The demand for client and server computing resources is better be represented as an XML block within the header of a TIFF file containing Attach Search 45. Olympus 3i SlideBook .sld balanced, allowing the same server hardware to handle more client the raw pixel data. This has been further extended to provide multi- le sessions concurrently. 46. Olympus CellR/APL .apl, .mtb, .tnb, .tif support. • The client engine can interact with the server without waiting for the 47. Olympus FluoView FV1000 .oib, .oif user to perform an interface action. This allows the user to view and As an extension to the data model we also provide formats for Semantic 48. Olympus FluoView TIFF .tif interact with the page asynchronously from the client engine's commu- Type Definitions and Structured Annotations. These provide the user with nication with the server. This option allows RIA designers to move data 49. OME-TIFF .ome.tif support to add their own types and data directly into the les in a format between the client and the server without making the user wait. 50. OME-XML .ome that our servers can interpret. • The network traffic may also be significantly reduced because an 51. PerkinElmer UltraView .tif, .2, .3, .4, ... application-speci c client engine is more intelligent when deciding OME Screen Plate Well 52. PICT (Macintosh Picture) .pict what data needs to be exchanged with servers. 53. PGM (Portable Gray Map) .pgm

54. PNG (Portable Network Graphics) .png Plate Well WellSample 55. Prairie Technologies TIFF .tif, .xml

Screen Reagent Manage Annotate 56. QuickTime Movie .mov Rate 57. SimplePCI .cxd ScreenAcquisition View History Search 58. TIFF (Tagged Image File Format) .tif The model has exible support for modelling the concepts used in high Attach Publish 59. VisiTech XYS .xys, .html content screening. Full information about these models is available online. Collaborate 60. Zeiss AxioVision ZVI (Zeiss Vision Image) .zvi Tag Personalize 61. Zeiss LSM (Laser Scanning Microscope) 510 .lsm

google: OME-XML http://www.ome-xml.org/ google: OMERO.web http://www.openmicroscopy.org/info/OMERO.web google: OMERO.editor http://www.openmicroscopy.org/info/OMERO.editor google: Bio-Formats http://www.loci.wisc.edu/ome/

The Open Microscopy Environment is a multi-site collabo- OME is developed as a joint project between research- Carl Zeiss Vision GmbH Nikon Inc. rative eort among academic labs and a number of active labs at the Dundee, NIA Baltimore, Harvard and Carl Zeiss, Advanced Imaging Microscopy Group OPIA commercial entities that produces open tools to support LOCI. In addition, OME has active collaborations with Center for Bio-Image Informatics Olympus America, Inc. data management for biological light microscopy. Our many imaging and informatics groups. Chroma Technology Inc. Omega Optical Inc. goal is to provide life scientists with open source access WE would like to thank the following organisations for Columbia University PerkinElmer Life and Analytical Sciences Inc. to sophisticated tools to support their work. Designed there contributions to the OME development effort: Escuela Superior Politécnica del Litoral SVision, LLC Laboratory for Optical and Computational Instrumentation to interact with existing commercial software, all OME Improvision Inc. Scientific Volume Imaging formats and software are free, and all OME source code is Applied Precision, LLC Intelligent Imaging Innovations, Inc. Universal Imaging Corp. available under GNU public "copyleft" licenses. Bitplane AG Leica Inc. Vanderbilt University School of Medicine