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Huygens Core

Powerfull compute engine for massive image processing via the CLI or HRM


Command Line Interface (CLI)

Huygens Remote Manager (HRM)




Multi-user access

Huygens renowned deconvolution and restoration accessible for many

Access via Web browser

Huygens Remote Manager (HRM) allows easy remote access to Huygens

Easy user management

Easily add and remove users, and keep track of the usage in HRM


Link to OMERO

Efficient image data exchange between HRM and OMERO

High-content/throughput

Ideally suited for batch image processing (deconvolution, restoration and analysis)

Visualization & Coloc

Peform Colocalization Analysis in batch mode, and visualize deconvolution results



Use Huygens Core with the CLI or HRM

Huygens Core full compute engine can now be called from any pipeline environment using our new Command Line Interface (CLI). Run Huygens sophisticated image processing tasks with a node/job managment software such as SLURMTM, or from an analysis pipeline scripted within, for example, JupyterTM. Combinations of different Workflow tasks can be created with Huygens and executed via the CLI. These tasks are also available in Huygens Workflow Processor (in Essential and Professional), and can include deconvolution, image stabilization, crosstalk and chromatic aberration correction, and also object analysis. For an overview of all the available tasks, see this webpage.

Huygens Core can be configured for maximum performance offered by computer nodes, large scale 64 bit multiprocessors, and systems with multiple (high-end) Nvidia GPU cards.


Use Huygens Core with Python or Tcl scripting

Huygens Core full compute engine can be directly accessed without a graphical user interface (GUI) using the Tcl shell window (left screenshot), or with a GUI presenting the enhanced Python or Tcl shells (right screenshot). These Python or Tcl shells, which are also available in Huygens Professional and Localizer, allow access to a fully functional Python or Tcl interpreter to manipulate images and perform many different operations. Furthermore, Python modules can be imported for even more functionality. A local Python installation is not required to use the Python interpreter. If you do not want to program yourself, you may just use a customizable front-end like the Huygens Remote Manager (see below).


Use Huygens Core with HRM

Huygens Remote Manager (HRM), is an open source task manager that acts as a web-interface to Huygens Core. It can be used with any web-browser, and is therefore ideally suited for scheduling many image processing (high content/throughput) jobs and serving many different users from any location. The user-friendly HRM interface accepts templates from Huygens Essential and Professional, and facilitates an optimized connection to OMERO (open source) image data servers for data import and export.

HRM is an open-source application developed by the Montpellier Rio Imaging facility, the Facility for Advanced Imaging and Microscopy at the Friedrich Miescher Institute (FMI, Basel), the BioImaging and Optics Platform at the Ecole Polytechnique Fédérale de Lausanne, and Scientific Volume Imaging.

Try out the HRM Demo!

HRM: The Queue Manager organizes job priorities

Includes tasks for deconvolution, restoration and colocalization analysis.
Import/export images from and to OMERO.
Supports various microscope types.
Handles many File Formats.
Automatic image parameter import from metadata.
User-friendly interface with step-by step guidance.
Image processing tasks are placed in a job queue.
Results can be explored online via interactive slicer and 3D previews.
Users receive email with a download link for the results.
Clear administration of users, including user statistics.


HRM: Batch image restoration and analysis

Huygens Remote Manager has built-in tasks for a complete image analysis pipeline. Besides deconvolution, tasks are available for hot/cold-pixel and bleaching correction, cropping, image stabilization, and chromatic aberration correction. Applying these restoration options further enhance the fidelity of any subsequent image analysis. Last but not least, HRM also offers you the possibility to include colocalization analysis in your imaging pipeline (see section below). After Huygens Core has succesfully completed a job, you will receive an email notification with a link to view the results. Online visualization tools for 2D slicing and the 3D previews HRM can be used to explore the results before you actually decide to download the resulting files.


HRM: Colocalization Analysis

HRM also offers the possibility to perform batch colocalization analysis. This colocalization task uses a pixel-based approach, and reports coefficients like Pearson, Spearman, Manders, and intersection. In addition, a 2D histogram of the image is presented, as well as a unique 3D colocalization map which facilitates the visual inspection of regions of colocalization within your image.


Tutorial and Download: get started!

The tutorial movies allows you to get started with the Huygens Remote Manager quickly. When you install the Huygens Suite on your computer, also feel free to try out our other products.

Tutorial Video Download Now!