[ome-users] Huygens Remote Manager 3.0 released!

Jason Swedlow j.r.swedlow at dundee.ac.uk
Fri Jan 18 19:12:27 GMT 2013

Hi Aaron-

Thanks for this update-- that's very exciting!

We'll add this to our web site. Any feedback our comments would be most welcome.

Regards to all at SVI!!



-----Original Message-----
From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Ponti Aaron
Sent: Thursday, January 17, 2013 5:38 PM
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Huygens Remote Manager 3.0 released!

Dear list,

today we released version 3.0 of the Huygens Remote Manager (http://huygens-rm.org). The HRM is a web interface for batch deconvolution performed by the Huygens software (http://www.svi.nl).

I'm forwarding the announcement e-mail (see below) to the OME users list to introduce the new interface to OMERO we implemented in HRM 3.0. The interface allows users to collect datasets to be deconvolved from an OMERO server instance and push back the deconvolution results to it.

It is an initial and quite simple implementation, but  we are planning to extend it based on users' feedback.

You will find information in the HRM installation instructions (http://huygens-rm.org/home/?q=node/6) and soon in the updated user manual (http://huygens-rm.org/home/?q=node/7)!

Thanks a lot for your attention,

for the HRM developers

Dr. Aaron Ponti
Software and Data Management Engineer
ETH Zürich
Department of Biosystems Science and Engineering (D-BSSE)
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch
+41 61 387 33 74

---------- Forwarded message ----------
From: Aaron Ponti <aaron.ponti at bsse.ethz.ch>
Date: Thu, Jan 17, 2013 at 4:52 PM
Subject: Huygens Remote Manager 3.0 released!
To: "hrm-list at lists.sourceforge.net" <hrm-list at lists.sourceforge.net>

Dear all,

I am very happy to announce the immediate availability of Huygens Remote Manager 3.0!

Yep, you read it correctly: because of the large number of major changes and added functionality, we decided to make this version of the HRM a new major release!

As I anticipated in a previous mail, this is the summary of the new features of HRM 3.0:

- 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

As usual, you can download the new HRM release from our download page: http://huygens-rm.org/home/?q=node/4.

Please notice that HRM 3.0 requires Huygens Core version 4.3.0-p2 or newer to run. You can get it here: http://www.svi.nl/Download.

A couple of additional words on some of the new features.

This release of the HRM starts a small revolution in the history of the HRM.

For the first time, the HRM goes beyond pure restoration and starts incorporating the analysis tools that you can find in the Huygens software. The first one we added to the HRM is the colocalization module, which creates very detailed and beautiful reports in the results page. More modules will be incorporated in the next releases, so stick with us!

As requested by several users for quite a while, we reversed the flow of job creation. First the files are chosen, and then the optical, restoration and analysis parameters are set accordingly.

The process of file selection has been reworked extensively and the confusing image geometry options have been eliminated.

An initial implementation of the HRM - OMERO interface is incorporated in HRM 3.0. Please mind that currently the OMERO server must run on the same machine as the web server. This limitation will be removed in the next releases -- also following your valued feedback!

The HRM will now check for existing, valid licenses in several places. In the system summary page (visible to the admin user), you can also get a summary of your license options.

Selecting a parameter set displays a preview of the parameters on the right - no more editing the parameter sets just to check which parameters were hiding in them!

All scaling factors are now cleanly reported in tabular form in the detail view of the deconvolution results.

The complete (svn) changelog can be found here: http://huygens-rm.org/home/?q=node/27.

The updated user manual (pdf) will follow soon! http://huygens-rm.org/home/?q=node/7.

Please mind that - as usually the case - HRM 3.0 will require a database and minor configuration file updates. The instructions can be found here: http://huygens-rm.org/home/?q=node/5

Complete installation instruction can be found here: http://huygens-rm.org/home/?q=node/6

Please refer to our contact page for any issue or request: http://huygens-rm.org/home/?q=node/8

I hope you will like this new version of the HRM!

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