HRM Hackathon 2016

Aaron Ponti Leave a comment

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!

Aaron Ponti Leave a comment

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

Aaron Ponti Leave a comment

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)!

 

 

HRM 3.2.2 released!

Aaron Ponti Leave a comment

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 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