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. Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software for parallel batch deconvolutions. For a more detailed introduction to deconvolution and the HRM please take a look at the dedicated publications.
Huygens Remote Manager (HRM) is intended for centralizing computational resources for the 3D deconvolution of images from wide-field, confocal, scanning-disk, single- and multi-photon and SPIM 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, restoration and analysis 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 from several microscopy file formats.
Authors and contributors
Original concept and implementation
- Pierre Travo and Volker Bäcker, Montpellier RIO Imaging (CNRS).
- Patrick Schwarb, now at Imagic AG, brought the original version of HRM to the Friedrich Miescher Institute (Basel).
- Aaron Ponti, Department of Biosystems Science and Engineering, ETH Zurich;
- Daniel Sevilla, Scientific Volume Imaging (Hilversum);
- Niko Ehrenfeuchter, Biozentrum (Basel);
- Olivier Burri, BioImaging and Optics Platform, EPFL (Lausanne);
- Torsten Stöter, Leibniz Institute for Neurobiology (Magdeburg)