HRM 3.10.0 released!

Today we released HRM 3.10.0, a fix release that also adds support for Abberior MSR and OBF file formats.

New features

  • Add support for MSR and OBF files.

Bug fixes

  • Fixed bug in dbupdate for shared templates.
  • Fix issue with container files in subfolders not having the used subimage in the result file name.
  • Fix issues with subimage previews.
  • Fix for 14-parameter chromatic aberration in user interface.
  • Fix for iteration and quality threshold in user interface.
  • Fix for inconsistent use of start and end time in statistics, now always using database time.
  • Fix destination image name by replacing : characters to _ characters, to prevent successful jobs to be reported as failing.
  • Improve handling of long file names.
  • Fixed the end time shown in the Log tab of the Details results.
  • Allow skipping creation of a Coloc map.
  • Fix reflected XSS in login form by removing obsolete hidden field.

Relevant links

Have fun with HRM 3.10!

HRM 3.5.0 released!

We are proud to announce the release and immediate availability of HRM 3.5!

The new HRM UI

The new features at a glance are:

  • New, modern user interface
  • GMLE deconvolution algorithm
  • Stabilization of deconvolved time series
  • New spherical aberration correction mode
  • New license overview page for admins
  • Performance increase for image selection
  • Bug fixes

As usual, please make sure that you follow the upgrade instructions carefully!

The following sections will provide some additional information on the new features of HRM 3.5.

New, modern user interface

HRM starts a major effort to give HRM a modern user interface that reduces the visual and functional gap with modern web applications. Besides aesthetic changes, also several functionality improvements are added to this release. More work is in the pipeline that will bring us to HRM 4.0.

GMLE deconvolution algorithm

HRM 3.5 adds support to Good’s roughness Maximum Likelihood Estimation, a new deconvolution algorithm that improves restoration of very noisy images (especially for STED and confocal data).

Stabilization of deconvolved time series

HRM 3.5 can optionally correct for cell motion, thermal drift, shaking, and other types of XYZ translations and rotations.

New spherical aberration correction mode

Fixing very strong spherical aberration is now possible thanks to the Huygens sub brick (varPsf) advanced correction mode (“Depth-dependent correction performed on few slabs”). Also, the spherical aberration correction is now always run if a refractive index mismatch is present.  A new image viewer helps with the selection of the coverslip position for the correction.

New license overview page for admins

A new overview page for admins lists the Huygens modules and options that are active on the system.

Performance patch for image selection

Scanning the image source folder with tens or hundreds of thousands of files is now orders of magnitude faster.

Have fun with the HRM 3.5!

HRM 3.4 released!

We are proud to announce the release of HRM 3.4! This release comes with a few big and many small changes in preparation for the release of HRM 4.0 that will be majestic!

The new features at a glance are:

  • Enhanced user management and security
  • Multi-GPU support
  • Chunked, parallel file uploader
  • Support for Metamorph ND and Leica LOF files

The following will describe the new features is some detail, but please make sure that you follow the upgrade instructions, since there were quite a few changes in this release!

Enhanced user management

HRM 3.4 offers several enhancements in the user management, that are only the beginning of more changes to come. In particular, we worked on the following points:

Enhanced security of user accounts

User credentials are managed and stored more securely in HRM 3.4 than in the past. But fear not: at the first login, the credentials will be transparently upgraded. So, no additional work is required for the users or the administrator(s)!

Multiple administrators possible

In HRM 3.4, multiple administrators are possible. The old ‘admin’ user still exists and has been upgraded to super admin (a super admin is an administrator that cannot be deleted and always has integrated authentication — see also below). The super admin and any other administrator in the system can then promote other users to administrators from the user management page.

Multiple authentication modes supported

In the past, you had to configure HRM to use one of three possible authentication mechanisms: the integrated, own HRM user management; Microsoft’s Active Directory; or generic LDAP. In HRM 3.4 you are no longer limited to one! For instance, you can use Active Directory for the bulk of your users, and use the integrated authentication for a handful of guest users. The one you have been using until now will become the default one on upgrade, and you can add more as explained in the instructions.

Multi-GPU support

In HRM 3.3 we added support for GPU deconvolution; in HRM 3.4 we extended that to support multiple GPUs! Please mind, however, that for multi-GPU support in HRM you will need to upgrade HuCore to version 16.10.1p0!

Also, configuration of processing servers and GPUs can now be performed by an administrator via the Servers & GPUs pages, and does not require modifying the database directly anymore!

New chunked, parallel file uploader

A new chunked file uploader allows uploading files larger than 2GB. Moreover, since chunks are uploaded over parallel connections, the speed of data transfer to the server should be improved.

Support for Metamorph ND and Leica LOF files

HRM 3.4 also expands on the palette of supported file formats by adding support for Metamorph ND (version 2) and Leica LOF files.

Some important remarks!

Do not extract the new archive on top of the previous installation!

In version 3.4, we started a major reorganization of the code structure of HRM and it is therefore highly recommended not to extract the new archive on top of the old one.

Please rename the old hrm folder, extract the code into a fresh ${HRM_ROOT} and move the configuration files from the old config subfolder into the new ${HRM_ROOT}/config.

You might also want to reinstall the hrmd or hrmd.service scripts.

Upgrade to mysqli driver

If your server runs PHP 5.6, please make sure to change the driver in the configuration files from mysql to mysqli, since the old mysql driver is deprecated in PHP5.6 and the apache log file will be seriously flooded with warnings!

Specifically, change:

// The database type (mysqli or postgres)
$db_type = "mysql";


// The database type (mysqli or postgres)
$db_type = "mysqli";

in config/hrm_{server|client}

Minimum Huygens Core version required

The minimum HuCore version has not changed from HRM 3.3. Please notice, however, that if you want to take advantage of multiple GPUs or would like to deconvolve Metamorph ND files, you will need to upgrade to HuCore version 16.10.1p0.

HRM upgrade instructions

The detailed upgrade instructions can be found here. Please follow the instructions carefully!

HRM download

You can download HRM 3.4 from the official download page!

HRM 3.3 released!

We are proud to announce the release of HRM 3.3! This release offers several new features such as chromatic aberration correction, SPIM deconvolution, GPU support, template import from data files and Huygens Suite, a much faster and powerful OMERO connector and much more!

Major new features in HRM 3.3

  • Create image templates from an image file
  • Import image templates from Huygens microscopy templates (.hgsm)
  • Import restoration templates from Huygens restoration templates (.hgsd)
  • Add support for GPU deconvolution
  • Add support for SPIM deconvolution
  • Add chromatic aberration correction
  • Faster and more powerful OMERO connector:
    • Complete rewrite in Python using the native OMERO API
    • Support for downloading multiple files at once from OMERO
    • Support for OMERO image previews
    • Status caching and on-demand loading to greatly speed up OMERO tree loading times
    • Support for OMERO users and groups hierarchy
    • Upload of HRM parameters along the deconvolved result images to OMERO
    • More interactive user interface (dialogs and status messages)
  • Add group authentication for Active Directory and generic LDAP
  • Add BigTIFF file formats “btf”, “tf2” and “tf8”
  • Support for 6 channels
  • New LSB-compliant HRM init and Queue Manager scripts
  • Remove deprecated ‘change_ownership’ variable

The following issues were fixed:

  • Clean stuck jobs from the queue on Queue Manager restart
  • Fix links to help pages for STED parameters
  • Fix issue with template names longer than 30 characters
  • Fix issue with processing server names longer than 30 characters
  • Remove dependency on php5-mysql when PostgreSQL is used
  • Fix broken icon links in Results/Preview section
  • Fix issue with the file upload button
  • Some more minor bug fixes

Minimum Huygens Core version required

For GPU- and SPIM-deconvolution support, HuCore version 15.10 is required. Otherwise, the same minimum requirement applies as for HRM 3.2 (14.6.1p7).

User manual

The user manual was updated to cover the new chromatic aberration, SPIM and GPU features, and the new template import functionalities.

HRM upgrade instructions

The detailed upgrade instructions can be found here. The upgrade procedure should not take more than a few minutes!

HRM download

You can download HRM 3.3 from the official download page!

HRM 3.2.2 released!

It is with great pleasure that we announce the immediate availability of HRM 3.2.2!

This patch release offers a faster parsing of sub-images in LIF files, it addresses some reported issues with files with blank spaces in their names, and fixes the many rendering issues that have historically been ruining the HRM experience in Internet Explorer (but please mind that you will need IE version 9 or more recent for this). The following is the complete 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 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