New features in Huygens Software

When not specified, changes apply to all Huygens Software products. Labels indicate particular products only: E = Huygens Essential, P = Huygens Professional, L = Huygens Localizer, S = Huygens Scripting, C = Huygens Core, T = Huygens Titan. For older release information see: WhatsNewArchive.

What's new in Huygens 19.04

New product: Huygens Localizer!

Huygens Localizer allows for easy and fast analysis of single molecule localization microscopy (SMLM) data:

  • Intuitive interface.

  • Automatic plots showing:
    • Bleaching patterns in the time series.
    • Particle counts per time frame.
    • Histograms of particle positions, intensity, offset, and uncertainty.

  • CPU and GPU support for fast analysis of SMLM data:
    • Background estimation
    • Spot detection
    • Localization
    • Rendering

  • Automatic drift correction and PPU estimation.

  • Export a table of localizations or use the interactive renderer to create super-resolution images.

  • Analyze SMLM super-resolution images.
    • Properties of the particles: position, volume, center of mass, surface, length, principal axes, etc.
    • Study groups of particles: distance to reference objects, intersection of objects in different channels, correlation, etc.

Huygens Professional & Essential

  • Abberior (STEDYCON) image feeder option:
    • Efficient data exchange from STEDYCON to Huygens.
    • Improved meta data interpreter.
    • Improved handling of single plane STED data.

  • GPU acceleration of
    • MIP, SFP (see below), and Surface renderers.
    • Many basic image operations (arithmetics, masks, thresholds, etc).

  • Complete overhaul of the SFP renderer:
    • Fast rendering on GPUs.
    • Much reduced memory usage.
    • New CPU functions.
    • GUI supports new lighting and shading options.

  • New Interactive 3D Fusion option (release candidate):
    • The tool is now in beta-testing phase, thus not yet in production. To try it out please contact sales at svi.nl for a test license
    • Manual approximate registration with the possibility for automatic fine tuning.
    • Deconvolve light sheet views while fusing them.

Minor changes
  • (E/P) Batch Express:
    • Add all output formats supported by Huygens.
  • (E/P) Preferences:
    • Ability to show only the beginning, end or both ends of long image thumbnail names.
  • (E/P) Colocalization Analyzer:
    • Addition of High Quality rendering option in the visualization tabs in Advanced and Compact modes.
  • (E/P) File open dialog:
    • Double click to instantly select and open a sub-image.
  • (E/P) Stitcher:
    • Add support for array detector images.

Bug fixes
  • (All) OBF and MSR readers:
    • Fix support for unsigned integer datatype.
  • (All) Image names:
    • Better handling of long image names in 'image create'.
  • (All) 'getframe' command:
    • Prevent command from working in-place.
  • (All) GPU processing:
    • Initialize the GPU memory when allocating new images.
  • (All) LIF reader:
    • Fix case where the file XML contains the history and parameters of the parent images.


(24th July 2019)

  • (All) GPU Processing:
    • Disable unintended GPU use by large median filters.
  • (E/P/C) Colocalization Analysis:
    • Fix minor memory leak.
    • Fix collision with the report of images open in Huygens.
  • (E/P/C) CMLE:
    • Fix regression on the padding of Widefield images with no spherical aberration.
  • (E/P) Object Analysis:
    • Fix highlighting, selecting and marking objects when rendering on high quality mode.


(17th July 2019)

  • (All) File readers:
    • Fix for uncommon ICS files missing the 'sensorChannels' parameter.
    • Fix for file types containing sub images with curly braces.
    • Fix for reading CZI Airyscan 2 files.
  • (All) CopyStretch ('cs') command:
    • Fix for the 'float -> byte' and 'complex -> byte' configurations.
  • (All) GPU Processing:
    • Add the NVIDIA "SUPER" cards.
  • (E/P/L) Filter commands:
    • Update cached image range used for image visualization.
  • (E/P/L) File Drag&Drop:
    • Fix for image names with special characters and patterns.
  • (E/P/L) Object Analyzer:
    • Clear removed objects which remained visible during analysis.
  • (E/P) Deconvolution Wizard:
    • Fix unimportant error message shown while loading templates.
    • Fix image stabilization of mixed STED/confocal or multichannel STED images.
  • (E/P) Deconvolution Express:
    • Fix potential error occurring when all GPU memory is used.
    • Show message when specific channels can't be processed due to lack of license.
    • Fix link to Twin Slicer. Opening the raw and deconvolved images in the Twin Slicer via the Deconvolution Express link should now show both images.
  • (L) Export tables:
    • Add option to toggle meta data export.
  • (L) Localization Analyzer:
    • Fix error when no options are selected in the candidate stage.
  • (L) Mac OS:
    • Add Localizer logo replacing the SVI logo.


(27th June 2019)

  • (All) GPU processing:
    • Relax the limit for the amount of extra memory that the cuFFT library is allowed to use to in order to use a regular 3D FFT in Cuda Toolkit version 10.1 update 1.
  • (All) Deconvolution:
    • Increase accuracy of non-widefield theoretical PSFs even further for very extreme cases.
  • (All) User preferences:
    • Fix default directory for saving images from within the Track Analyzer.
    • Fix inconsistent behaviour in the GPU window.
  • (All) 'ctm' command:
    • Fix the ctm command to not return an error caused by parsing sn and snr options that do not exist for this command.
  • (L) Localizer:
    • Keep the render button always active.
    • Fix occasional error in drift correction.
    • Fix center and fit after crop.
    • Fix histogram of multi channel images.
    • Starting the tool via a right-click incorrectly skipped the microscopic parameter check.


(3rd June 2019)

  • (L) Installer:
    • Added code signing for Localizer.
  • (All) File readers:
    • Fix file read failures in the dv/mrc reader (due to the use of uninitialized memory).
    • Fix the hdf5 file reader when reading single-channel hdf5 files written by other software.
  • (E/P) Batch Processor:
    • Fix different handling of microscopic parameters depending on how the template is loaded.


(21st May 2019)

  • (All) Windows OS:
    • Remove occasional KMP warning about load balancing of threads.
  • (All) User Preferences:
    • Add option to enable/disable dynamic thread balancing.
  • (All) GPU processing:
    • More lenient GPU license limits w.r.t. amount of VRAM (see GPUCards).
  • (All) Gaussian filtering:
    • Increase performance of 'qgauss' for several CPUs and image geometries.
  • (All) ND2 reader (Linux/Mac):
    • Fix for uncommon dimensions.
  • (E/P/L) GPU processing:
    • Prevent "invalid data spec" error in operations where the 'cp' command is used on the GPU.
    • Show several secondary messages as warnings instead of as errors.
  • (E/P/L) Cropper:
    • Fix some unusual inconsistencies in the cropping box and spinboxes.
  • (E/P) MIP renderer:
    • Fix occasional off-centered scene.
  • (E/P) Colocalization Analyzer (all forms):
    • Fix widget not showing completely due to lack of space.
  • (C) SFP top views:
    • Remove the SVI logo from the scene table.
  • (L) Localization Analyzer:
    • Fix optional histogram in the segmentation pane.
  • (L) Localizer:
    • Add option for higher accuracy fits (see Particle localization -> Expert -> Fitting).
    • Progress bar shows progress more often.

Huygens Remote Manager 3.6

The highlights of this release are:

  • New Array Detector deconvolution (a.o. Airyscan and nanoSPAD)
  • New Rescan deconvolution
  • New UI dark theme
  • Performance and stability improvements in the job queue
  • Compatibility upgrade to PHP 7.2
    • Please notice that this is the last HRM release to support PHP 5.x which was officially discontinued at the end of 2018!

HRM 3.6 also brings along some other changes:

New Array Detector deconvolution

HRM has been extended to support one of the most requested new features in Huygens: array detector deconvolution. Therefore, Huygens 18.10 is needed for deconvolving this type of data in HRM. For more information about the array detector option in Huygens see https://svi.nl/Array-Detector.

New UI dark theme

In the previous version (3.5), HRM started a major effort toward a modern user interface. In this new version, we continue down that path by releasing a dark theme that makes HRM more gentle on the eyes of those doing deconvolution right from within the dark room. But of course, you can use it everywhere!
If the UI shows any glitches at first, please clear the browser cache.

Have fun with HRM 3.6!
(source http://www.huygens-rm.org)

For older release information see: WhatsNewArchive.

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Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands

Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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