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From Huygens-rm.org
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News
| May 25th, 2010: | HRM 1.2.3 released! Download it! |
| May 17th - 21th, 2010: | HRM at the Huygens User Group Meeting (17th-18th) and at the 10th ELMI meeting (18th-21th). |
| April 15th, 2010: | HRM 1.2.2 released. |
| April 12th, 2010: | Simple configuration checker (integrated in HRM 1.2.2): Usage: php check.php /path/to/hrm_server,client_config.inc |
| April 9th, 2010: | Patch for HRM 1.2.1 released (integrated in HRM 1.2.2). |
| April 6th, 2010: | HRM 1.2.1 released.' |
| April 2nd, 2010: | Created hrm-list mailing list! You can subscribe here! |
Old News...
Introduction
Nowadays, deconvolution in cell and tissue imaging has matured into a standard restoration technique that is accessible to large fraction of the microscopy community thanks to steadily improving algorithms. Still, deconvolution is often the rate-limiting step in the analysis of the acquired data, even at today's computer performance. The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software for parallel batch deconvolutions.
References
- A. Ponti, A. Gulati, V. Bäcker and P. Schwarb. Huygens Remote Manager: a Web Interface for High-Volume Batch Deconvolution. Imaging & Microscopy 9(2):57-58, 2007
- Unabridged version of the previous paper (pdf)
Feature overview
The Huygens Remote Manager (HRM) is intended for centralizing computational resources for the 3D deconvolution of images from wide-field, confocal or scanning-disk fluorescent microscopes. You can use HRM with any recent web browser.
HRM will lead you via its web interface, step by step, in entering the microscopic and restoration parameters necessary for deconvolving your images. These parameters are stored in collections of settings, so that they can be used multiple times. Then HRM will put your deconvolution tasks (multiple files in a go, if necessary) into a job queue.
The independent HRM queue manager will process the tasks in the queue (running on the same web server, or on other computing-dedicated servers) and notify the different users by email when their results are available.
The results can be explored via the web browser before downloading the files, to compare them with the raw images and control the quality of the restoration. (You may decide that a deconvolution is necessary with different parameters, and discard the current results, without having to download them). A preview of the 3D stack can also be downloaded as a convenient AVI movie.
HRM can ask Huygens Core to deconvolve 2D, 3D images, and time series in the following microscope file formats:
- Delta Vision (*.dv)
- SVI HDF5 (*.h5)
- Image Cytometry Standard (*.ics/*.ids)
- Image Cytometry Standard 2 (*.ics)
- Imaris Classic (*.ims)
- Leica LIF with sub-images (*.lif)
- Zeiss (*.lsm)
- OME-XML (*.ome)
- Biorad (*.pic)
- Metamorph (*.stk)
- Zeiss Vision ZVI (*.zvi)
- Olympus FluoView TIFF
- Leica TIFF series
- Numbered TIFF series
- Single XY TIFF plane
Authors and contributors
Original concept and implementation
- Pierre Travo and Volker Bäcker, Montpellier RIO Imaging (CNRS).
Current developers
- Patrick Schwarb (initiatior) and Aaron Ponti (developer and current project coordinator), Friedrich Miescher Institute, Basel (FMI);
- Alessandra Griffa, École Polytechnique Fédérale de Lausanne (EPFL);
- José Viña, Scientific Volume Imaging, Hilversum (SVI).
Former developers
- Asheesh Gulati, École Polytechnique Fédérale de Lausanne (EPFL);
Testing the HRM
You can find some screenshots of the HRM at the SF project page and at the SVI support server.
A HRM for demo purposes is installed at the SVI support server, with some tiny test images in the source directory. It is not intended to show the deconvolution capabilities of Huygens but the usability of the HRM interface. Still, you may pay attention to the deconvolution parameters and try to obtain good results from these test images!
Please apply for a user account by following the instructions at the login page, or simply use the guest account, with username guest and password hrmsvi.
Go to the HRM demo server
License
The Huygens Remote Manager is open-source software, released under the conditions of the CeCILL License.
Download
The HRM code can be downloaded from the SourceForge site. It is very much recommended that you follow the Download and Installation instructions.
