HRM 3.7.1 released!

HRM 3.7.1

It is with great pleasure that we announce the immediate availability of HRM 3.7.1!

This patch release addresses a few issues:

  • Jobs (including colocalization analysis) may sometimes miss the colocalization results when all the following conditions are met:
    • the processing machines have multiple GPUs;
    • the queue is processing 2 or more jobs from the same user in the same machine;
    • the raw images of these jobs are located at the same directory level.
  • For new HRM installations we have fixed an incompatibility issue with recent versions of PostgreSQL. This should not affect existing installations.
  • The automatic Linux updates often shut down the HRM deamon service, not starting it again after the update. This has been improved and therefore it is recommended to reinstall the HRM daemon service by following these simple steps

As usual, you can download HRM 3.7.1 from the official download page:

Happy deconvolving!

HRM 3.7.0 released!

Huygens Remote Manager 3.7.0

It is with great pleasure that we announce the immediate availability of HRM 3.7.0!

This release focuses primarily on performance and stability, but it also introduces some new features.

Detailed changes of HRM 3.7.0 are:

  • Allow image channels to be assigned the restoration algorithm individually or skipped altogether.
    This adds the possibility to use HRM as a pure batch file converter, chromatic aberration corrector, time stabilizer, etc.
  • Add an “All files” filter in the image selection step. Show by default all the contents of the raw images folder.
  • Add extreme GPU support.
  • Replace old EPFL logo with current.
  • Substantially increase performance of files listing.
  • Substantially increase performance of job creation.
  • Make queue more robust against job deletion, process killing, process failure, and stalling.
  • Switch to persistent connections to the database.
  • Cache many database query results to reduce traffic.
  • Bug fixes.

Please notice that we decided to maintain compatibility with PHP 5.6 for this release, but from the next release the minimum supported PHP version will be 7.2.

Go ahead, and download it!

HRM 3.6.0 released!

We are very happy to announce the release and immediate availability of HRM 3.6!

The new dark theme

The highlights of this release are:

  • New Array Detector deconvolution (a.o. Airyscan and nanoSPAD)
  • New Rescan deconvolution
  • New UI dark theme
  • Performance and stability improvements in the job queue
  • Compatibility upgrade to PHP 7.2
    • Please notice that this is the last HRM release to support PHP 5.x which was officially discontinued at the end of 2018!

HRM 3.6 also brings along some other changes:

New Array Detector deconvolution

HRM has been extended to support one of the most requested new features in Huygens: array detector deconvolution. Therefore, Huygens 18.10 is needed for deconvolving this type of data in HRM. For more information about the array detector option in Huygens see

New UI dark theme

In the previous version (3.5), HRM started a major effort toward a modern user interface. In this new version, we continue down that path by releasing a dark theme that makes HRM more gentle on the eyes of those doing deconvolution right from within the dark room. But of course, you can use it everywhere! 
If the UI shows any glitches at first, please clear the browser cache.

Have fun with HRM 3.6!

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 3.5.0 teaser

A teaser for the upcoming 3.5.0 release with a brand new UI and a lot of new functionality!

HRM 3.5.0 welcome page

Click to enlarge

The major new features in HRM 3.5.0 are:

  • New, modern user interface
  • GMLE deconvolution algorithm
  • Stabilization of deconvolved time series
  • New spherical aberration correction modes
  • Performance patch for image selection
  • Bug fixes

HRM 3.4.1 released!

The HRM 3.4.1 patch release addresses the following issues:

  • Fix bug with admin not being allowed to login if the database has not been upgraded yet.
  • Fix issue with checkConfig.php script mistakenly reporting that $authenticateAgainst is not an array even if it is.
  • Fix regression with querying global statistics.
  • Fix logger initialization in OmeroConnection.
  • Allow the admin to add server entries with no GPUs.

Go ahead and download it – and do not forget to carefully follow the upgrade installations!

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 Hackathon 2016

Another successful HRM Hackathon is over!

As in the last two editions, this year’s HRM Hackathon was hosted by Roland Nitschke at the Life Imaging Center of the Center for Biological Systems Analysis in Freiburg (D).

In an intense five-day effort, we continued working on some running projects and kick-started some new ones.

In particular, a new set of installation scripts that automate most of the installation steps of the HRM will be released very soon.

The new Queue Manager based on the gc3pie tools and libraries is almost complete and is planned to be released in HRM 4.0 hopefully in fall 2016.

A completely reworked user management system with strongly enhanced security will be soon released in HRM 3.4.

Work is in process to integrate a graphical file manager in the HRM UI, which is in turns being completely rewritten! Release time for the new file manager has not been defined yet.

Stay tuned!

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 Hackathon 2015

The 4th HRM hackathon is over. And it was a very productive one!

Indeed, this year we tackled both short-term and ambitious long-term tasks.

Among the most immediate tasks, we fixed a couple of post-3.2.2-release issues. We will release them soon together with the upcoming 3.3 release (Summer 2015).

For 3.3, we also implemented the option to import image templates from selected files and from templates created in the Huygens Suite. Correction for chromatic aberrations will be optional in the Restoration menu. Also, we will release the new installer scripts that will greatly simplify the setup of HRM.

Directly from our middle-term plans, a completely new Queue Manager will be the highlight of HRM 4.0 (End 2015).

And even bigger surprises are coming in HRM 5.0 (after Hackathon 2016)!