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. For older release information see: WhatsNewArchive.

What's new in Huygens 19.10

Huygens Localizer

  • New option for analyzing astigmatic 3D SMLM data:
    • Support for CPU and GPU.
    • PSF Distiller for obtaining nearly noise-free 3D SMLM calibration data from fluorescent beads.
    • MIP Renderer with depth-coded color modes.
    • 3D object analysis.
  • New Batch Processor for 2D SMLM data:
    • Process large amounts of data in batch mode.
    • Support for CPU, GPU, and multi GPU.
    • Optionally save the localization tables and renders of each batch job.

Huygens Professional & Essential

  • New Huygens Fuser:
    • Replaces the Fusion Wizard which can now be found in Tools -> Legacy.
    • Manually align multi-view light sheet images with direct visual feedback.
    • Fully tunable automatic optimization on manual alignment.
    • Pre-cropping result image for a more memory efficient and faster fusion.

  • Many new features in 3D rendering and performance improvements:
    • New CPU implementations with perspective for all renderers to allow seamless switching between CPU and GPU.
    • Freely adjustable lighting direction in the SFP Renderer, as well as a camera-tracking mode.
    • The ability to add an iso-surface to a scene in the SFP Renderer, allowing you to highlight important features.
    • The ability to add up to 6 cutting planes to a scene in the SFP Renderer, each with a configurable orientation and offset. Cleanly cuts away SFP material and iso-surfaces.
    • The slicer in the Surface Renderer now actually cuts away surfaces.
    • New depth-coded color mode in the MIP Renderer. Each point is assigned a hue based on either the Z-position or the distance to camera.

  • New render panel in main window:
    • Real time views for the selected image thumbnail showing 3D scenes from the MIP, SFP and Surface renderers, plus the 2D plane from the center of the stack.
    • The views also serve as links to the corresponding tools (MIP renderer, SFP renderer, Surface renderer, Twin Slicer).
    • Optionally collapse/expand the render panel.

Minor changes
  • (All) Abberior STEDYCON:
    • Better decisions in case of occasional communication problems (e.g., network issues).
    • Improved deconvolution of images with extremely high saturation factors.
    • The saturation factors reported via the Parameter Editor, Huygens Tcl commands, etc., now reflect the values used by the deconvolution and the Abberior acquisition software.
  • (All) License Manager:
    • New possibility to add/remove licenses without the need to restart Huygens.
  • (All) GPU support:
    • Even more functionality is now supported by the GPU (qgauss filter, resample, binning).
    • Automatic migration of images to and from the GPU makes better decisions.
    • New GPU status indicator in the case of a missing CUDA Toolkit.
  • (All) Parameter Editor and related Huygens Tcl commands:
    • Added new microscope types TIRF and SMLM 3D for Localization microscopy (no deconvolution).
  • (All) TIFF reader:
    • Much faster loading of TIFF series on Windows.
  • (E/P) Decon Express & Batch Express:
    • Better decisions for images with all parameters verified by the user (see Parameter Editor).
  • (E/P) PSF Distiller:
    • New colored overlay showing accepted versus rejected beads.
    • Report on the reasons for rejecting each discarded bead.
    • Larger thumbnails for candidate and accumulated images.
  • (E/P) Object Tracker/Track Analyzer:
    • Show total track length of joined segments.
  • (E/P) Slicers:
    • Rename gamma options 'Stretching' -> 'Apply to', 'Global' -> 'Full image', 'Per screen' -> 'Displayed region'.

Bug Fixes
  • (All) Deconvolution:
    • Increase accuracy of non-widefield theoretical PSFs even further for extreme cases.
  • (All) File readers on Windows:
    • Fix the calls to the OS in order to avoid the 'Not responding' stamp.
  • (All) 'avgspheres' command:
    • Fix small memory leak.
  • (All) DV/MRC Reader:
    • Distinguish better between reading tiled images and time series.
    • Improved reading of tile offsets.
  • (E/P) Analyzer tools:
    • Update ROI selection to work with perspective rendering. An ROI is now represented by a shallow cone.
  • (E/P) Cropper:
    • Fixed unexpected frame-number rounding behavior when trimming very small time series.
  • (E/P) Stitcher:
    • Fixed occasionally incorrect patterns after loading tiff series.


(26th March 2020)
  • (All) LIF reader:
    • Fix for meta data of TIRF data sets.
  • (All) HDF5 reader:
    • Fix potential errors on unknown meta data fields.
  • (All) Colocalization analysis:
    • When RBNCC is selected do the processing on the CPU.
  • (P/C) 'genPsfExpl' command:
    • Made 'stedInhibContr' parameter optional.
  • (E/P) Stitcher:
    • Fix regression for FOVs showing tiles with lots of signal as well as tiles with only background and noise.
  • (E/P) 2D visualization tools:
    • More defensive against potential errors on image statistics.
  • (E/P) SFP renderer:
    • Add missing parameters to movie transitions of small images.
  • (P) Operations Window:
    • Rename 'regularization' as 'signal/noise ratio' where needed.


(27th January 2020)

  • (All) Deconvolution:
    • Fix regression in high quality ICTM algorithm.
    • Fix reading of default template values for cropping and stabilization tasks.
    • Better handling of Array Detector time series.
    • Better handling of 1-plane widefield images.
  • (All) 'stat' command:
    • Add GPU support for extra dimensions.
    • Fix potential out-of-bounds issue in GPU implementation.
  • (All) 'gauss' command:
    • Better optimizations for 1-pixel-high images.
  • (All) GPU license:
    • Grant free GPU usage to Quadro T1000.
  • (All) CZI reader:
    • Only set the array detector properties when there's more than one detector.
  • (All) IMS writer:
    • Fix to not write uninitialized memory to the file header.
  • (E/P/C) Batch Processing:
    • More robust against 'stdout' errors potentially leading to task timeouts.
  • (E/P) Main window UI:
    • Set the 'histogram' tab as the new default tab.
    • In Professional switch to the 'Task reports' tab and back to the previously selected tab automatically when there's work being done.
  • (E/P) Chromatic Aberration Corrector:
    • Allow for 3 decimal point factors.
  • (E/P) Deconvolution Express:
    • Fix a bug in the PPU estimator that could result in a Tcl error and no deconvolution result.
  • (E/P) Batch Express:
    • Fix for irrelevant warning.
  • (C) SNR estimator for HRM:
    • More accurate results.


(2nd December 2019)

  • (E/P) Interactive Fuser:
    • Fix issue in background handling for the first processed view.
    • Weighted sum of local pixel value now correctly weighs the overlapping regions instead of simply adding them.
  • (E/P/L) Thumbnails:
    • Improve scaling of thumbnails and reinstate 2D option for smaller thumbnails.
    • Fix 3D SMLM results sometimes only being shown as 2D thumbnails in Localizer main window.
  • (E/P) Object Analyzer:
    • Include new option for filtering objects touching only X or Y borders.
  • (All) RPM Installer:
    • Fix missing application menu and desktop icons after upgrading Huygens for future versions.
  • (All) GPU initialization:
    • Add version check for CUFFT library and distinguish NVIDIA graphics driver Cuda version from Cuda Toolkit version in the GPU status window.
  • (All) File readers:
    • Added support for stitching of LaVision OME-TIFF tile-series with [00 x 00] filname pattern.
    • Improve bit-depth checks for better reading of .czi files.
    • Fix for .dv files with 16-bit data that could not be loaded.

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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