Talk 8-Kevin-Imagej2
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The LOCI laboratory develops new optical instrumentation and software to study living specimens dynamically in 3D. It has been a partner in the Open Microscopy Environment project since 2003. The laboratory focuses on multidimensional fluorescence, spectra, and lifetime imaging and analysis. It leads development of the open-source Bio-Formats and ImageJ software projects for reading diverse bioimaging data formats and processing/analyzing images. The laboratory currently includes several programmers working on these projects and seeks to integrate quantitative imaging with systems biology.
Talk 8-Kevin-Imagej2
- 1. Kevin Eliceiri Laboratory for Optical and Computational Instrumentation www.loci.wisc.edu eliceiri@wisc.edu
- 2. Mission of LOCI New optical instrumentation to facilitate studies of the dynamics of living specimens. Better software for capture and visualization of dynamic, 3-D biological events Been OME Development partner since 2003 Image Informatics for multidimensional data spatial and temporal spectral and lifetime dimensions polarization
- 3. Fluorescence, Spectra, Lifetime (λ,τ) Time-Lapse (t) Phase, Polarization, Scatter, Harmonics (φ, θ,…) Chemistry Physics Dynamics Space (x, y, z) Optical Microscopy Structure Supporting Technologies Hardware Acquisition software Analysis and Visualization Data Management Our data:
- 4. LOCI OME Informatics Group- 2012 Curtis Rueden Lead ImageJ2 Melissa Linkert Lead Bio-Formats (Glencoe Programmer in residence) Johannes Schindelin Lead FIJI, ImageJ2 and OME developer Barry Dezonia ImageJ2 Developer Jimmy Fong Lifetime Analysis Researcher Aivar Grislis ImageJ2 Developer Mark Hiner SCIFIO Developer Kristin Briney OME XML Metadata Graduate Programmer
- 5. • Specific OMERO linked applications • BK Cho in Murphy lab on Omero.searcher • Forward Project for data dissemination • Originated OME-TIFF in 2004 • Now fully integrated into OMER0 • Used by many open and commercial tools • Our current focus on robust tools to read and write OME-TIFF • Originated Bio-Formats in 2005 • partnership with OME and Glencoe • Over 120 formats • Over 30,000 installations • Recent focus on native bindings • XML Schema Improvements for Acquisition and Analysis • Our WiscScan software and now MicroManager • Plans to extend to others that want richer OME-TIFF • Interoperability between OME and other tools (FarSight, CellProfiler, FIJI, ImageJ • ImageJ 2.0 (ImageJDev.org) Overview of our OME efforts:
- 6. Bio-Formats: the tool for interoperability
- 7. Open Source Toolkit Development
- 8. Why ImageJ2? Support the next generation of image data Interoperate and collaborate with other projects Broaden the ImageJ community Reuse each others' work wherever practical Provide a central online resource for ImageJ - Program downloads, a plugin repository, developer resources and more
- 9. Who Develops ImageJ2? And anyone who wants to contribute!
- 10. Guiding Principles Preserve backwards compatibility Maintain good performance Support N-dimensional imaging Use common input and output for data Minimize complexity Employ open source software dev. practices
- 11. ImageJ 2.0.0-beta2 Supports most ImageJ1 plugins and macros Many new pixel types Multidimensional data beyond 5D Import and export of many file formats Improved region of interest (ROI) tools Truly headless Automatic updates Easily install additional plugins (e.g., Fiji >350 plugins!) 175 new/reimplemented core ImageJ2 plugins so far
- 12. Data Model Based on ImgLib2 library Any data source (files, URLs, DBs...) N-dimensional images Unlimited pixel types Write algorithms once
- 13. Displays and Visualization The user interface provides views of the data Show multiple datasets in one window Or multiple windows showing the same dataset Composite any # of channels Fully pluggable
- 14. Regions of Interest ROIs are functions that identify samples upon which to operate Overlays are visuals superimposed over a dataset, often (but not always) linked to ROIs
- 15. User Interface Provides widgets for several UI styles: - Swing - “Pure” AWT - Eclipse SWT - Apache Pivot Custom UIs possible Can run headless Use ImageJ2 as a library to execute plugins
- 16. Interoperability
- 18. Service Architecture Plugins Events Animation I/O Displays Overlays Tools Platforms UIs Options Core ImageJ2 Services Custom Service Another Service ImageJ Context
- 19. ImageJ Updater Keeps ImageJ2 plugins up-to-date Installs new plugins Anyone can create an update site and upload their own plugins to it Compatible with existing Fiji update sites (including fiji.sc)
- 20. Data I/O Uses SCIFIO (SCientific Image Format Input & Output) library for reading and writing data New formats can be added as SCIFIO plugins
- 21. Launcher Many options for launching ImageJ2 Run scripts in batch mode Multiple platforms Run headless
- 22. Future Directions Release one beta per month Big green button Easier development Better integration with native code Website: central plugins listing Application-driven development
- 23. ImageJ2 What can ImageJ2 already do? (as of June 2012)
- 24. ImageJ2: Data Model • Driven by powerful ImgLib2 processing library • Support for many new data types
- 25. ImageJ2: N-Dimensional • Support for more than five dimensions • Composite more than seven channels • Improved math equation editor
- 26. ImageJ2: Spectral Lifetime Analysis • SLIM Plugin for visualizing and analyzing combined spectral lifetime image data • Works with data in time domain • Available from LOCI update site
- 27. ImageJ2: Updater • Central mechanism for installing new plugins • Compatible with Fiji update sites
- 28. ImageJ2: Updater • Install and use Fiji plugins • 3D Viewer, Bio-Formats, more
- 29. ImageJ2: Updater • Can work with third party update sites too • On right, VisBio Ortho Stack plugin from LOCI update site
- 30. ImageJ2: Customizable UIs • Multiple user interfaces possible • Swing, AWT, Apache Pivot, Eclipse SWT… • Support for Swing Look & Feels • Metal, Motif, Nimbus, Aqua, Windows, GTK, etc.
- 31. ImageJ2: Launcher • New launcher with many more features • Based on Fiji’s launcher • Single, multi-platform distribution of ImageJ
- 32. ImageJ2: Interoperability • Separate data model from user interface • Plugin framework works completely headless • Enables integration with other tools: • CellProfiler (see next slide) • KNIME Image Processing • OMERO servers and clients
- 34. • SCientific Image Format Input & Output • SCIFIO is simply the core of Bio-Formats • Isolates core from PFFs and OME data model • Convert other scientific imaging data models • Provided under Simplified BSD License • Bundled with ImageJ2, ITK, VisAD… • Bio-Formats becomes a “SCIFIO plugin” • Core Project of OME • Recently funded by NSF
- 35. ImageJ2, FIJI OME Hackathons
- 36. Acknowledgements Principal Investigators • Kevin Eliceiri (LOCI), Rudolf Oldenbourg (MBL), Anne Carpenter (Broad), Jason Swedlow (Dundee) Pavel Tomancak (Dresden), Bob Murphy (Carnegie Mellon), Badri Roysam (U. Houston). Developers • Curtis Rueden, Grant Harris, Barry DeZonia, Aivar Grislis, Mark Hiner, Johannes Schindelin (ImageJ2) • Lee Kamentsky, Adam Fraser (CellProfiler), Melissa Linkert (Bio-Formats) Collaborators • Wayne Rasband (ImageJ) • Albert Cardona (Fiji) • Stephan Preibisch, Stephan Saalfeld (ImgLib, Fiji) • Mark Longair, Jean-Yves Tinevez (Fiji) • OMERO development team (OME) • Glencoe • Michael Bethold and KNIME team Funding: NIH ImageJ2 Grant NSF SCIFIO Grant Wellcome Trust Open Microscopy Environment Grant
- 37. Image Informatics Postdoctoral Position @LOCI Announcement: Computational Postdoctoral Position at the Laboratory for Optical and Computational Instrumentation (loci.wisc.edu). • Position integrates quantitative imaging, image informatics in systems biology study. • The project will leverage and add to many of the open source toolkits in use and development at LOCI including the Open Microscopy Environment, and FIJI ImageJ projects. Please email Kevin Eliceiri eliceiri@wisc.edu if interested.