What's new?

Changelog HRM 3.2.0 to HRM 3.2.1

Bug fixes

  • Folder named '0' is not listed in the file selector.
  • Paths containing single quotes block the 'Select images' drop down.
  • Support for Active Directory Forests breaks standard AD authentication.
  • SNR estimator lists no images for OME-TIFF input format.
  • The bin/hrmd and bin/hrm_user_manager scripts in the archive did not have the execute permission active.
  • User directory creation is broken when "sudo" is not configured.

Requirements

  • HRM 3.2.0 requires Huygens Core 14.6.1-p9 or newer to run!

Changelog HRM 3.1.1 to HRM 3.2.0

Requirements

  • HRM 3.2.0 requires Huygens Core 14.6.1-p7 or newer to run!
  • A database update is required for HRM 3.2.0!

New features

  • Added templates sharing mechanism for parameters and PSF files
  • Vastly extended and optimized OMERO integration in the HRM
  • Added (conservative) autocropping option
  • Migrated HRM (installation) documentation to readthedocs.org
  • Standardized setup - Please review your installation!
  • Added support for multi-tile CZI files
  • Enhanced support for complex Active Directory set-ups
  • Added Zeiss LSM 780 to the backprojected pinhole calculator
  • From the login page it is now possible to register to HRM mailing list
  • Loads of minor tweaks and fixes

Changelog HRM 3.0.3 to HRM 3.1.0

Requirements

  • HRM 3.1.0 requires Huygens Core 4.5.1-p1 or newer to run!
  • A database update is required for HRM 3.1.0!

New features

  • STED deconvolution support
  • Nikon ND2 file format support
  • Custom lens immersion medium refractive index
  • Selection lists (files, templates, ...) are now resizable
  • Faster ZIP creation for downloading results
  • Report issues button
  • Improved navigation bar
  • Back-projected pinhole calculator for Leica SP8
  • Mailing list now uses BCC instead of TO

Changelog HRM 3.0.2 to HRM 3.0.3

Requirements

  • HRM 3.0.x requires Huygens Core 4.3.0-p2 or newer to run!
  • A database update is required for HRM 3.0.3!

New features

  • Added support for Zeiss CZI file format
  • Increased the size of the "Go to detailed results" link

Bug fixes

  • ActiveDirectory.inc.php leaked socket connections
  • Output TIFF 8 / 16 / RGB was visible for time series
  • Incompatibility with preg_match() in PHP 5.4
  • An entry in the FileExtension table contained a blank too many
  • Killing jobs could lead to the QM stalling
  • Misconfiguration of ActiveDirectory could lead to user credentials being displayed in the browser

Changelog HRM 3.0.1 to HRM 3.0.2

Requirements

  • HRM 3.0.x requires Huygens Core 4.3.0-p2 or newer to run!

Bug fixes

  • Fixed bug #103: Error message containing raw credentials on LDAP (AD) failure.
  • Fixed bug #102: SNR estimator lists no images on OME-TIFF input format.
  • Fixed bug #99: Output TIFF 8 / TIFF 16 should not be available for time series.
  • Fixed some rendering problems with the OMERO browser.
  • Relaxed limitation on characters allowed in passwords.
  • Fixed parsing of the quality change criterion in the parameter table.

New features

  • The admin can now check for the availability of updates from within the HRM.
  • Added JSON-RPC functionality to allow more powerful asynchronous calls.
  • The error e-mail contains a better explanation of the cause of failure at the beginning of the text.
  • Better handling of 2D datasets and time series.
  • Added "Send test e-mail to admin" to check proper configuration of the e-mail server.
  • Limited the number of jobs displayed in the queue table to 100 to prevent the application getting stuck in retrieving and updating the table.
  • Enhanced name sorting of file series.

Changelog HRM 3.0.0 to HRM 3.0.1

Requirements

  • HRM 3.0 and 3.0.1 require Huygens Core 4.3.0-p2 or newer to run!

New features

  • Fixed handling of Metamorph STK file series
  • Fixed file refresh issue in the file browsers
  • Fixed dynamic update of the queue

Complete svn changelog.

Changelog HRM 2.1.2 to HRM 3.0

Requirements

  • HRM 3.0 requires Huygens Core 4.3.0-p2 to run!

New features

  • Restructured the HRM workflow, that now starts with file selection
  • Added the "Analysis" step to the workflow, which features the first of more tools to come: colocalization analysis
  • The HRM can now get data from and push the deconvolution results back to an OMERO server
  • Added parameter set preview (no need to edit parameters to see the details)
  • Added checks for licensed modules and summary of licenses in the admin view
  • Deconvolution and data type scaling factors are now reported in the results page (parameters view)
  • Made the raw data and results sections more prominent
  • Made the Queue Manager more robust against killed and failed jobs
  • Replaced the confusing image geometry with 'file series'
  • Cleaned the confusing TIFF options
  • Added RGB TIFF 8 bit output file format
  • Added Ajax calls in several places to make the HRM quicker and more responsive
  • Updated all external libraries
  • Loads of minor changes and bug fixes

Complete svn changelog.

Changelog HRM 2.1.1 to HRM 2.1.2

Requirements

  • HRM 2.1.2 requires Huygens Core 4.1.0-p2 to run!

Bug fixes

  • Fixed Javascript regression that broke the refresh and delete buttons
  • Fixed several Javascript and layout problems with Internet Explorer 8 (and partially 9)
  • Fixed permissions on src/hrm_previews that would prevent thumbnails to be deleted if queue manager and web interface are run as different unix users
  • Fixed problem with algorithm selection reverting to QMLE when coming back from the SNR estimator and QMLE is the algorithm saved in the database
  • Fixed problem with SFP movies never created for time series

Complete svn changelog.

Changelog HRM 2.1 to HRM 2.1.1

Requirements

  • HRM 2.1.1 requires Huygens Core 4.1.0-p2 to run!

Bug fixes

  • Fixed bug [3463362]: Launching the SNR estimator crashes IE8

Complete svn changelog.

Changelog HRM 2.0.3 to HRM 2.1

Requirements

  • HRM 2.1 requires Huygens Core 4.1.0-p2 to run!

Summary of new features

  • Changed the mechanism by which parameters can be overridden at run time: now parameters with high confidence can just be omitted in the HRM templates and their values will be read from the files at run-time.
  • When opening one of the calculators (e.g. SNR calculator), the values already typed in won’t be lost; moreover, the calculated values will be fed back to the calling pages (this uses a client-side mechanism to mimic cross-page posting using session storage).
  • Added simple mechanism to allow users to customize the HRM login page (by creating a user/home_user.inc file).
  • Added a simple check to bin/hrmd to prevent starting more than one instance of the queue manager.
  • Extended summary page with the output of phpinfo() (nicely displayed into the standard HRM layout).
  • The statistics page now uses a nicer calendar widget to filter stats by date with one-day resolution.
  • Updated the adLDAP library to version 4.0.3.
  • Extended and fixed LDAP support. Now user groups can be queried. Changes in the configuration files needed! Please follow the explanations in config/samples/ldap_config.inc.sample.
  • Restructured and cleaned the file manager;
  • The Ubuntu font replaces Verdana;
  • The HRM renders much better on Internet Explorer (>=8);
  • Used parameters are now displayed in a beautiful table in the file manager.
  • If the database is not up-to-date, the admin is directed directly to the database update page (bypassing home) at login.
  • Added warning to the upload action in the file manager: the user should be careful when uploading ics files not to forget the ids (and vice versa).
  • Added more navigation options between pages.
  • Added mechanism to reset radio buttons (i.e. to unselect all with one click) for parameters with low confidence.
  • MacOSX: added resources/hrmd.plist.sample (to replace hrmd.plist).
  • Changed home page link ‘Manual’ to ‘User manual’.
  • Added notification in the home page for newly created jobs.
  • Added mechanism to rename copied template parameters if their name collides with existing user parameters.
  • Cleaned the email notifications.
  • The selection of a default parameter set can now be reset.

Bug fixes

  • Fixed bug [3412158]
  • Fixed bug [3419516]
  • Fixed issue with deleting settings in chrom{e|ium}.
  • Fixed a problem with passwords when a user is created by the administrator.
  • Rewritten the 'image geometry quick help' that was making users believe they could reshape the geometry of the loaded datasets.
  • HRM was ignoring whether file uploads were enabled or disabled in php.ini and only using the $allowHttpUpload variable in the configuration files (which is obviously subordinated to php.ini).
  • CSS fix for Chrom{e|ium} browsers not wrapping multi-channel input fields in filedsets.
  • Fixed a bug in the year range for statistics filtering.
  • Made dbupdate.php more robust against mistakes if more databases with the same structure exist (e.g. hrm and hrm_test).

Complete svn changelog.

Changelog HRM 2.0.2 to HRM 2.0.3

HRM 2.0.3 (like its predecessor 2.0.2) requires Huygens Core 4.0.1-p0 to run!

  • Fixed bug 3432651: Failing jobs in HRM 2.0.2 if working with HuCore 4.1.0p3

Complete svn changelog.

Changelog HRM 2.0.1 to HRM 2.0.2

Please mind that HRM 2.0.2 requires Huygens Core 4.0.1-p0 to run!

  • Fixed bug 3390619 [hucore]: problem with deconvolution of ics files
  • Fixed bug 3390394 [hucore]: failed parsing of Stk time series
  • Fixed bug 3314124: user allowed to pick Imaris as output format for time series
  • Fixed bug [hucore]: inefficient generation of time-series SFP movies for XY-time datasets
  • Fixed several more minor issues

Complete svn changelog.

Changelog HRM 2.0 to HRM 2.0.1

Please mind that HRM 2.0.1 requires Huygens Core 3.7.1-p6 to run!

  • Fixed bug 3298194: filtering by time was not working for some of the statistics
  • Fixed bug 3304459: creation of z and time strip previews would fail for very large datasets
  • Fixed bug: deconvolution of 2D time series would fail
  • Minor code cleaning and refactoring

Complete svn changelog.

Changelog HRM 1.2.3 to HRM 2.0

This is a short summary of the changes between HRM 1.2.3 and HRM 2.0:

  • Extensive refactoring of several core HRM classes and of the user interface
  • Implemented communication to hucore through hucore templates (this requires hucore 3.7.1-p2 or newer); all legacy code to generate old fashioned hucore scripts was removed
  • Implemented support to deferring reading of metadata information to hucore; parameters in the HRM may be overridden at runtime (this mechanism relies on confidence levels for parameters in file metadata)
  • Added system summary page in the admin backend that lists versions, php.ini settings, configuration values,...
  • Reorgainzation and cleaning of configuration files; updated resources/checkConfig.php to test configuration files
  • Added new SNR estimator (in beta) along with the classic one
  • Documented all code: current API on http://api.huygens-rm.org/html/
  • Enhanced hrmd daemon to support more usage configurations (to make it easier to start the queue manager as boot not as root)
  • Updated all external libraries to latest versions
  • Added a lot of input form validation
  • Removed the MRI accounting system
  • Added a Javascript-only mechanism to get dynamic help on all pages
  • The HuCore version is now stored in the database
  • Extended file manager to display the log of the deconvolution jobs and a summary of the parameters used
  • Added support for DeltaVision r3d file format
  • Log-ins are now logged
  • Loads of bug-fixes and minor enhancements

Complete svn changelog.