Deconvolution Software

Huygens Essential Image Processing Software, version 3.5

Huygens® Essential is an image processing software package tailored for deconvolution of microscopy images with the ease of use of a wizard‐driven intelligent user interface.

It deconvolves a wide variety of images ranging from 2D widefield (WF) images to 4D multi-channel multi-photon confocal images. Its dual 4D slicer tool facilitates comparison of raw and deconvolved data, or comparison of results from different deconvolution runs.

Its powerful and fast renderers produce different representations of your data, not needing any special graphic card.

It is available for the Microsoft® Windows® and Apple Mac OS™ X operating systems and for other platforms.

Key Features

• Five‐stage guided deconvolution procedure;
• Extensive image parameter checking;
• Creates image histograms to spot problems due to saturation early on;
• Automatic functions:
  • Estimation of the background;
  • Bleaching correction;
  • Deconvolution of time series;
  • Correction for spherical aberration;
  • Z-drift correction;
• Guides you along multi‐channel deconvolution;
• Comparison viewer enables you to inspect and compare images;
• Thumbnail representation of images in progress;
• Standard up to 32 channels;
• You can measure, store and deconvolve using your own point spread function (PSF);
• Reads files in many formats:
• Writes files in common formats:
• Comes with one full year of maintenance;
• Remote display
  • via Remote Desktop Protocol if running on Microsoft® Windows® operating system;
  • via X11 protocols if running on Mac OS™ X or Linux;
• Automatic and manual cropping of datasets in five dimensions (3D + time + channels);
• Visualization renderers:
  • Twin Slicer: easy comparison of original and deconvolved data, or of different slices in your data;
  • Fast Maximum Intensity Projection (“MIP”) renderer: instant spatial MIP of your data;
  • Volume renderer (“SFP Renderer”): produces physically realistic 3D representations of your data;
  • Surface Renderer: for easy exploration of the different objects present in your data via maximum intensity projection or isosurface rendering;
• Movie Maker creates sophisticated animations of your multi‐channel 3D images:
  • Uses the Fast MIP, Surface or SFP renderers;
  • Produces separate TIFF sequences or AVI files;
  • AVI files work with Windows Media Player, Apple QuickTime™, VLC, MPlayer, any other MJPEG‐enabled player;
• 32‐bit version available for:
  • Linux, on Pentium III‐class computers or better;
  • 32‐bit editions of the Microsoft Windows XP and Windows Vista operating systems, on Pentium 4‐class computers or better;
  • PowerPC or Intel Mac OS X 10.4 “Tiger” and 10.5 “Leopard.”
• 64‐bit version available for:
  • X86‐64 computers running Linux;
  • X86‐64 computers running 64‐bit editions of the Microsoft Windows XP and Windows Vista operating systems;
  • PowerPC or Intel Mac OS X 10.5 “Leopard.”
• Datasets:
  • 32‐bit version supports 2 GB datasets; 2 GB or more RAM is recommended.
  • 64‐bit version supports datasets up to 12 GB, with commensurate RAM.

Processing Stages

The Huygens Essential Wizard performs processing in stages:

• Parameter Checking
• Cropping
• Image Histogram Checking

In the first pre-processing stage, the intelligent parameter checker scrutinizes the microscopic parameters obtained from the source image. It marks suspicious optical conditions, warns of undersampling conditions, then asks for confirmation of those parameters.

The confirmed parameters may be saved in a parameter template for future re-use in other images.

In the next stages you can use the automatic cropping tool, inspect the image histogram to spot clipping or saturation and inspect the image background.

The image histogram is an essential tool for detecting clipping and inspecting the image background level.

Intelligent 4D cropping tool

The 4D cropping tool allows you to trim images along four dimensions and to delete uninteresting channels. This conserves memory and applies the computer’s processing power to the interesting parts of the image.

Nonetheless, situations occur in which your system’s memory is not sufficiently large to allow the image to be deconvolved as a whole. In these cases the image is split into “bricks.” Huygens Essential deconvolves the bricks one by one and assembles the results seamlessly into a deconvolved whole.

Point Spread Function Generation

With Huygens Essential it is possible to load a measured Point Spread Function (PSF) to deconvolve your images. When a measured PSF is not available, Huygens Essential automatically uses a theoretical PSF. This theoretical PSF is computed from the microscopic parameters that Huygens Essential has obtained from your image and that you have then confirmed. Because a theoretical PSF can be generated without any user intervention, Huygens Essential does the calculation in the background without any notice.

Step by Step Deconvolution

The wizard guides you in deconvolving the different data channels in a interactive way. You can vary the restoration parameters if you wish, comparing the image restoration results with the original data using the Twin Slicer. When all the channels are restored, you can merge them easily to save the final image.

Visualization and Analysis

Apart from the image restoration tools described in this article, Huygens Essential also has optional tools for Volume Visualization and Interactive Analysis. These include the Surface Renderer, the Simulated Fluorescence Process (SFP) Renderer and the Movie Maker.

The Surface Renderer enables you to represent your microscopy data in a convenient way to clearly see separated volumes. It is not only capable of isosurface rendering; it is also able to show MIP projections together with the surfaces to be used as a reference to the original microscopic voxel data.

The Simulated Fluorescence Process (SFP) Renderer is based on taking the 3D microscopy image as a distribution of fluorescent material, simulating what happens if the material is excited and how the subsequently emitted light travels to the observer.

The Movie Maker is a tool that allows you to easily create sophisticated animations of your multi‐channel 3D images using the powerful SFP, MIP, and surface renderers. The AVI movies can be played by Windows Media Player, Apple Quicktime, and other players that support the MJPEG standard.

Image File Formats

Huygens Essential reads many file formats; the Extended File Formats Option adds support for reading further formats.

Formats that every installed Huygens Essential reads:

• HDF5
• ICS, ICS2
• OME
• TIFF
  • Multi-layer TIFF
  • Leica numbered name TIFF series
  • Numbered name TIFF series
  • Olympus ‘Fluoview’ TIFF
  • Olympus SIS TIFF series
• MetaMorph STK
• Bio‐Rad PIC
• MRC
  • DeltaVision R3D, DV
  • IVE IMSubs
• Imaris classic

Formats included with the the Extended File Formats Option:

• Zeiss ZVI
• Zeiss LSM
• Leica LIF files
• Olympus OIF
• IPLab TIFF
• IPLab IPL
• IPLab IPM
• iVision‐Mac IPM

Formats in which Huygens Essential writes:

• HDF5
• ICS
• ICS2
• OME
• Imaris classic
• Biorad PIC
• MRC
  • DeltaVision R3D and DV
  • IVE IMSubs
• TIFF
  • Eight‐bit, 16‐bit, or RGB 24‐bit pixel data
  • Single‐image file, multi‐image file or series of files given Leica numbered names

Demonstration software is available from Scientific Volume Imaging’s Web site.

Deconvolution references are available.