HRM 3.2.2

Changelog

New features

• Faster parsing of LIF files
• Added PSF type to summary table
• HRM now renders correctly in Internet Explorer 9 and above
  • IE 8 and older are no longer supported!
• The image preview page now shows the file name
• New huygens-rm.org official website!

Bug fixes

• Fixed broken template sharing in IE
• Fixed issue with the measured PSF selection tool showing each file twice
• Fixed issue with blank spaces in names breaking the file selection field in FF and IE
• Plenty of minor fixes

Documentation

• Migrated HRM User Manual to readthedocs.org: http://huygens-remote-manager.readthedocs.org/en/3.2.2/
• Added more documentation about measured PSF files

HRM 3.2.1

This patch release fixes following bugs:

• 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.

To upgrade, follow the instructions on http://huygens-remote-manager.readthedocs.org/en/latest/upgrade.html.

As mentioned for the 3.2.0 release, the ownership and permissions on the HRM data folders must now follow the supported configuration. Please make sure that you follow the instructions on http://huygens-remote-manager.readthedocs.org/en/latest/hrm_conf.html#set-up-the-hrm-user-and-group, or you might encounter various file access issues.

To temporarily revert to the old mechanisms (that required the configuration of /etc/sudoers!) you can set a configuration variable $change_ownership = true in the configuration files as described on http://huygens-remote-manager.readthedocs.org/en/latest/upgrade.html#update-the-configuration-files. Please mind that this is deprecated and will be removed in HRM 3.3.0!

Please also notice that we updated and added quite a lot of new documentation on http://huygens-remote-manager.readthedocs.org/en/latest/. Please refer to these instructions for setting up and maintaining the HRM. We would also highly appreciate if you reported any errors, missing or confusing parts in the documentation!

For HRM 3.2.1, the recommended Huygens Core version is 14.06.1-p9 or higher.

HRM 3.2.0

HRM 3.2.0 comes with several new features and plenty of fixes and tweaks.

The major new functionalities in HRM 3.2.0 are:

A new template sharing mechanism

This allows user to share image, restoration and analysis templates with each other, thus adding a social twist to the HRM ;-) It also shares PSF files associated with the templates.

A vastly extended integration of the HRM with OMERO

The HRM can now interface with a remote OMERO installation at higher performance than in HRM 3.1. For more information about the new OMERO connector, please see our poster at the OME Meeting 2014: http://downloads.openmicroscopy.org/presentations/2014/Paris-Posters/Poster-10-Ehrenfeuchter-HRM.pdf.

A (conservative) autocropping option

Autocropping optimizes deconvolution time and memory load for large datasets that present extensive backround regions at the borders that do not carry valuable information.

Migrated documentation

We migrated the installation documentation to readthedocs.org (http://huygens-remote-manager.readthedocs.org/en/latest/). The user manual will also be posted on readthedocs.org soon.

Standardized setup

Please review your HRM installation!

We are trying to consolidate and standardize the way the HRM is meant to be installed and configured as a requirement for major future HRM features. Specifically, the system users running the Queue Manager and the web server are expected to have direct read-write access to the data folders. This basically means that both running the Queue Manager as root and Method 2a on http://huygens-rm.org/home/?q=node/18 will stop working.

In method 2a, the web server user is granted rights to run specific commands (/bin/mkdir, /bin/chown, /bin/chmod, /bin/rm ) via /etc/sudoers. From HRM 3.2.0 on, the Queue Manager and the web server users are expected to be allowed to run those commands directly without sudo rights.

Please notice that HRM 3.2.0 defaults to the new behavior; if you need more time to migrate, you can temporarily force the old behavior by adding the line:

$change_ownership = true;

to the config/hrm_server_config.inc and config/hrm_client_config.inc configuration file (see config/samples/hrm_server_config.inc for more info). Please mind that this behavior is obsolete and will be removed in HRM 3.3.0.

A complete list of new features can be found on http://huygens-rm.org/home/?q=node/27

Requirements

Please notice that HRM 3.2.0 requires the freshly released Huygens Core version 14.6.1-p7 (or newer): please go ahead and download it from http://www.svi.nl/download. It also requires a database upgrade: please login as the administrator after you have updated the HRM code and you will be led directly to the "Database update" page.

Have fun!

HRM 3.1.1

REQUIREMENTS

(o) HRM 3.1.1 requires Huygens Core 4.5.1-p1 or newer to run.

CHANGELOG

BUG FIXES

(o) The possibility to select from the available PSFs was not offered any more.
(o) The file server needed to set the default image extensions first. This call was missing.

HRM 3.1.0

REQUIREMENTS

(o) HRM 3.1.0 requires Huygens Core 4.5.1-p1 or newer to run.
(o) A database update is necessary.

CHANGELOG

NEW FEATURES

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

BUG FIXES

We also fixed several bugs. One in particular is worth mentioning here:

(o) LDAP connection uses exclusively protocol version 2