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OMERO Changelog

What's new in OMERO 5.1.3

Aug 21, 2015
  • Improvements include:
  • tagging actions extended; you can now use tag sets to tag images on import
  • tagging ome-tiff images at import has also been fixed
  • greatly improved workflow and bug fixes for the Share functionality in OMERO.web which enables you to share images with users outside of your group (including removal of part of the UI)
  • group admins and owners can now change ownership of data via the CLI
  • better reporting for the 'delete' and 'chgrp' functionality in the CLI
  • fixed display of images in plates with multiple acquisitions
  • fixed export of results as .xls files from OMERO.insight
  • improved workflow for ImageJ and OMERO interactions
  • fixes for ROI display in OMERO.web (thanks to Luca Lianas of CRS4)
  • fixes and workflow improvements for running scripts and script dialogs
  • Developer updates include:
  • OMERO.web clean-up (removal of '-locked')
  • reorganization of the server bundle to move various licenses and dependencies under a new 'share' folder
  • refactoring of 'Chown2', 'Chmod2', 'Chgrp2' and 'Delete2'
  • addition of dynamic scripts
  • the 'rstring' implementation is now more lenient and should better handle unicode
  • Bio-Formats submodule removed from OMERO; decoupling effort means OMERO now consumes the Bio-Formats release build from the artifactory
  • Sysadmin updates include:
  • support for WSGI OMERO.web deployment (FastCGI will likely be deprecated in 5.1.4 and removed for 5.2)
  • fixed OMERO.mail service for web errors

New in OMERO 5.1.2 (May 28, 2015)

  • BIO-FORMATS:
  • Adds writing support for OME-TIFF to the native C++ implementation, allows export of OME BigTIFF, and adds a Slidebook6 reader (many thanks to Richard Myers of 3i - Intelligent Imaging Innovations).
  • OTHER IMPROVEMENTS INCLUDE:
  • improved MATLAB developer documentation
  • preliminary work to make MATLAB toolbox work with Octave
  • ImageJ fixes for getPlanePosition* macro extension methods and display of composite color virtual stacks
  • many bug fixes for formats including:
  • Nikon ND2 - improved parsing of plane position and timestamp data
  • TIFF - reduced memory required to read color lookup tables
  • Zeiss LSM - improved parsing of 16-bit color lookup tables
  • Zeiss CZI - fixed ordering of original metadata table and reading of large pre-stitched tiled images
  • AIM - fixed handling of truncated files
  • Metamorph/MetaXpress TIFF - improved UIC1 metadata tag parsing
  • Leica LIF - improved metadata handling

New in OMERO 5.1.1 (Apr 28, 2015)

  • improved performance of ImageJ plugin when working with ROIs
  • TIFF export - switch to BigTIFF if .tf2, .tf8, or .btf extensions are used
  • fixed upgrade checking to more accurately report when a new version is available
  • Many bug fixes for formats including:
  • Zeiss CZI - fixed ordering of multiposition data and improved support for RGB and fused images
  • Nikon ND2 - improved ordering of multiposition data
  • Leica LIF - improved metadata validity checks and excitation wavelength detection
  • Metamorph STK/TIFF - record lens numerical aperture and fixed millisecond values in timestamps
  • Gatan DM3 - correctly detect signed pixel data
  • Imaris HDF - fix channel count detection
  • ICS export - fix writing of files larger than 2GB

New in OMERO 5.1.0 (Apr 14, 2015)

  • New key-value pairs annotations for adding experimental metadata
  • Improved workflow for rendering settings and parity between the clients
  • Import images to OMERO from ImageJ and save ROIs and overlays from ImageJ to OMERO
  • Changing groups and delete operations are now faster
  • Import times are much improved for large datasets
  • OMERO.mail lets admins configure the server to email users
  • Configurable server download policy for controlling the download of original files
  • Many developer updates such as removal of deprecated methods, updates to OMERO.web and the C++ implementation
  • Improvements to performance with network file systems
  • Improvements to developer documentation
  • Initial version of native C++ implementation
  • Improved support for opening and saving ROI data with ImageJ
  • Added support for CellH5 data (thanks to Christophe Sommer)
  • Added support for Perkin Elmer Nuance data (thanks to Lee Kamentsky)
  • Added support for Amnis FlowSight data (thanks to Lee Kamentsky and Sebastien Simard)
  • Added support for Veeco AFM data
  • Added support for Zeiss .lms data (not to be confused with .lsm)
  • Added support for I2I data
  • Added support for writing Vaa3D data (thanks to Brian Long)
  • Updated to OME schema 2015-01
  • Update RandomAccessInputStream and RandomAccessOutputStream to read and write bits

New in OMERO 5.0.8 (Feb 10, 2015)

  • This release fixes one specific issue causing OMERO.insight to crash when trying to open the Projection tab for an image with multiple z-stacks.

New in OMERO 5.0.7 (Feb 4, 2015)

  • Rendering improvements including 32-bit and float support
  • Vast improvements in Mac launching (separate clients for your Java version)
  • Faster import of complex plates
  • OMERO.dropbox improvements
  • ROI and measurement tool fixes
  • OMERO.matlab updates

New in OMERO 5.0.6 (Jan 22, 2015)

  • Bug fixes:
  • Pixel sign for DICOM images
  • Image dimensions for Zeiss CZI and Nikon ND2
  • Support for Leica LIF files produced by LAS AF 4.0 and later

New in OMERO 5.0.5 (Sep 25, 2014)

  • Fixed Security Vulnerabilities:
  • 2014-SV2 Empty Passwords:
  • Password-related security vulnerability affecting versions of OMERO4 up to and including 4.4.11 and OMERO5 up to and including 5.0.4.
  • 2014-SV1 Unicode Passwords:
  • Password-related security vulnerability affecting versions of OMERO4 up to and including 4.4.11 and OMERO5 up to and including 5.0.4.

New in OMERO 5.0.4 (Sep 4, 2014)

  • For OMERO:
  • fixes for Java 8 issues - both the OMERO clients and OMERO.server should now be compatible with this Java update
  • a fix for uploading masks in OMERO.matlab
  • Bio-Formats improvements include:
  • multiple fixes for the .ND2 formats
  • Java 8 fixes
  • support for PicoQuant .bin files (thanks to Ian Munro)

New in OMERO 5.0.3 (Aug 6, 2014)

  • further improvements to the searching functionality in all the clients.
  • group owners may adjust group permissions.
  • Webclient: Group user switching now works on tablets and handles long group/user lists better.
  • Webclient: Downloading of original files is now available when multiple images are selected.

New in OMERO 5.0.2 (May 28, 2014)

  • For OMERO users, this release includes:
  • Import improvements especially for large image datasets;
  • Allowing rendering settings to be shared between users;
  • Downloading original files from the command line;
  • Improvements to the way OMERO.matlab handles annotations;
  • Improvements to tagging workflows in the clients;
  • Further work on code signing for webstart and accompanying documentation;
  • Disk space usage reporting for OMERO.web admins;
  • Custom webstart intro page templates;
  • Enabling searching by Image ID in the clients.
  • Developers, script creators, and other power users should note that we've adopted flake8 formatting for all Python code contributions. Further:
  • the Java build dependencies have been aligned more closely with Maven Central
  • there are two new CLI commands, "obj" for creating and editing objects, and "fs" for seeing an overview of your data imported into OMERO5
  • a number of script improvements.
  • For system administrators, changes include:
  • modification to the import template path
  • the addition of "bin/omero ldap create" to create LDAP users before they login
  • fix for the periodic failure of the script process
  • various fixes for issues on Windows with testing up to version 2008 Server. A build of Ice 3.5 is now also available for testing.

New in OMERO 5.0.0 (Mar 25, 2014)

  • The 5.0.0 release represents a major change in how the OMERO server handles files at import compared with all previous versions of OMERO. Referred to as 'OMERO.fs', this change means that OMERO uses Bio-Formats to read your files directly from the filesystem in their original format, rather than converting them and duplicating the pixel data for storage. Images saved in an OMERO 5.0.0 repository can be accessed by other 3rd party software (this is read-only access). OMERO also now reports on the file integrity at upload so you know if your file is safely stored.
  • Bio-Formats 5.0.0 includes substantially improved handling of complex multidimensional datasets, including tile-based formats used in digital pathology and support for several new file formats; Aperio AFI, Inveon, MPI-BPC Imspector, Bio-Rad SCN, Yokogawa CellVoyager [1], LaVision Imspector, PCORAW, and Woolz [2].
  • In addition, 5.0.0 continues our effort to support new multidimensional images. We previously enabled support for FLIM data in OMERO.server, and the FLIMfit application built by the Imperial team. We've now added support for FLIM data in OMERO.insight.
  • The changes in Bio-Formats and OMERO 5.0.0 are especially important for sites working with large multi-GB datasets, e.g., long time lapse, HCS and digital pathology data. With this foundation, we will deliver support for other multidimensional modalities (e.g., light sheet microscopy) later in 2014.
  • For Bio-Formats:
  • Launched 'bioformats_package.jar', a new bundled plugin for ImageJ to replace 'loci_tools.jar';
  • Added support for 8 new formats (see above);
  • Fixed support for Becker & Hickl .sdt files with multiple blocks;
  • Fixed tiling support for TIFF, Hamamatsu .ndpi, JPEG, and Zeiss .czi files;
  • Added support for populating and parsing ModuloAlong{Z, C, T} annotations for FLIM/SPIM data;
  • Many bug fixes (especially Nikon ND2, Zeiss .czi, CellWorX);
  • Updated Bio-Formats tools command line documentation;
  • Updated component names, .jar file names, and Maven artifact names;
  • Improved continuous integration testing.
  • For OMERO:
  • Support for password salting to improve server security;
  • Updated indexing to help improve search performance;
  • OMERO.web upgrade to Django 1.6 allowing more flexibility for developing new web apps;
  • Initial steps towards supporting MATLAB and Jython scripts;
  • CLI plugin allowing access to tags and tag sets from the command line;
  • Modulo (FLIM/SPIM) support in OMERO.insight;
  • Many bug fixes including thumbnails, plates, tables and LDAP;
  • New help guide for installing the plugins needed to use OMERO with ImageJ;
  • 'What's New' summaries for users, sysadmins and developers to help you quickly identify updates.

New in OMERO 4.4.10 (Jan 20, 2014)

  • improved tile-loading
  • better network-disconnect handling
  • more flexible webapp deployment
  • Ice 3.5.1 support (except on Windows)
  • numerous bug fixes, especially during the modification of metadata, users, and groups.

New in OMERO 4.4.9 (Nov 5, 2013)

  • fixing compatibility issues between clients and servers using different Ice versions e.g. client using Ice 3.5 connecting to a server using Ice 3.4;
  • adding Ice 3.5 support;
  • updating minimum system requirements to Java 1.6 (Java 1.5 is no longer supported);
  • a major reworking of the testing infrastructure;
  • new scripting sharing service as requested by users;
  • new user help website to host workflow-based guides;
  • new partner project pages to highlight work going on within the extended OME consortium.

New in OMERO 4.4.8 (May 3, 2013)

  • Fixed two specific issues:
  • a problem with the OMERO.insight client for Linux [1]
  • image thumbnails not loading for Screens/Plates in Private/Read-Only groups in OMERO.web [2]

New in OMERO 4.4.7 (Apr 26, 2013)

  • usability and performance improvements in viewing of 'Big' tiled images;
  • new permission features - import data and assign to another user ('Import As'), view all data from all users in a group at once;
  • OMERO.web support for 'Split View Figure' and 'Thumbnail Figure' creation;
  • OMERO.web support for copy-and-paste of rendering settings;
  • addition of several utility functions in the OMERO.matlab toolbox to load and manipulate objects from the server;
  • review and testing of the C++ bindings;
  • improved checksum calculation to detect errors on file upload;
  • and the addition of array columns in OMERO.tables.

New in OMERO 4.4.4 (Nov 2, 2012)

  • Deliverables:
  • OMERO.insight:
  • Increased connection and configuration options for use as a plugin, tagging on import
  • Editor fixes
  • ImageJ and Java Web Start fixes. Removal of old ImageJ code.
  • ROI and Shape fixes
  • OMERO.web:
  • big image and roi viewer fixes
  • extended chgrp functionality
  • improved admin functionality
  • landing page links (#8299)
  • and various other bugs including 404s, rendering/zooming, thumb layout, batched annotations,
  • OMERO.server:
  • Improved handling of LDAP ":attribute:" types
  • Improved VM and homebrew deployments
  • fixed minor memory leaks and unclosed handles
  • Minor fixes to pyinotify for DropBox?
  • Fix for file downloads above 2GB and fs-lite handling of Leica SCN
  • Various permission fixes
  • JDK5 fixes
  • OME-XML:
  • #9344 RGB fixes
  • #9565 t/z slice fixes
  • And reference handler fixes.