High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
Huygens
Huygens logo

Description

The Huygens Suite is a complete and easy to use microscopic image restoration (deconvolution) package. Whether applied to images from a wide field (conventional) microscopes, confocal microscopes, 2-photon microscopes, the software in The Huygens Suite will remove blur from your images, improve resolution and reduce noise. It is capable of recovering lost details in very noisy confocal images. Applied to wide field images it will drastically remove blur and improve resolution.

How to Use

Huygens requires an X-windows session. Click here for more information about X-Windows.

Huygens is licensed to run on a single node in the Biowulf cluster, and only with fixed allocated resources. There are three "levels" of allocation: Small, Medium, and Large. The necessary level depends on your processing needs. Each level allocates a fixed number of GPUs and CPUs. To run Huygens, allocate an interactive session with the chosen level, along with an appropriate amount of memory. The memory allocated can be any amount up to 240g (GB).

By default, an interactive session is given 8 hours. If you need more than that amount of time to finish your processing, you should include --time in your allocation. For example, to allocate 16 hours of time to your Medium session, type:

[biowulf]$ sinteractive --constraint=huygens --gres=gpu:k80:2 --cpus-per-task=28 --mem=128g --time=16:00:00

Once an interactive session has been started, load the Huygens module:

[cn4243]$ module load Huygens
[+] Loading Huygens 17.04.0-p6 ...
[cn4243]$ huygenspro

When finished, make sure to exit the program and the interactive session:

[cn4243]$ exit
[biowulf]$

There are multiple versions of Huygens available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail Huygens

To select a module, type

module load Huygens/[ver]

where [ver] is the version of choice. This will set your $PATH variable to allow the Huygens executables.

Type the following commands at the prompt to start the corresponding programs:

Disk Space

By default, huygenspro writes to your /home directory. Since /home is limited is disk space, it would be best to create a symlink to your /data directory from the beginning:

mkdir /data/$USER/SVI
ln -s /data/$USER/SVI /home/$USER/SVI

Documentation

Click on the 'Help' menu on the far right of the Huygens window after launching the application.

Web-accessible: SVI (Scientific Volume Imaging). Also see the SVI Support Knowledge Base. For access to the restricted online tutorials at the SVI wiki, contact staff@hpc.nih.gov for the group login and password.