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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, C = Huygens Core. For older release information see: WhatsNewArchive.





What's new in Huygens 21.10

Huygens Professional, Essential, Localizer & Core


You can also watch the new Huygens features and improvements in the WhatsNew webinar.

Object Analyzer: Full version available in Professional and Essential, basic version available in Localizer
  • Add the possibility to use the lasso tool to merge objects.
  • Add two new reported parameters for counting objects that are contained in an objects in the other segmentation group. The parameter iParent reports the label a child object is contained in, the parameter iChiCnt reports the number of child objects contained in the parent object. These two new parameters are included in the "Colocalization (intersection)" experiment preset.
  • Improve performance of the analysis itself, especially for parameters related to distance to surface (up to 45 times faster) and parameters related to nearest neighbors (up to 6 times faster).
  • Add buttons to the main Object Analyzer window for exporting the ROI to the main menu and for redoing actions.
  • Improve formatting and readability of the result table.
  • Improve handling of very large objects.
  • (E/P) The "PS" segmentation mode has been removed.
  • For watershed segmentation, the initial sigma for the gaussian filter is now estimated based on image properties.
  • (E/P) In the Workflow Designer in the Object Analyzer, add more options for modifying the ROI.
  • (L) the Object Analyzer Basic now contains a second segmentation group for analyzing two channels at once.

Workflow Processor (E/P/L)
  • (E/P) It is now possible to do Stitching with the Workflow Processor.
  • (E/P) Create and edit Stitching templates in the Workflow Designer for the Workflow Processor.
  • Customize which templates are shown in the Workflow list in the Workflow Processor.
  • Improvements in the user interface of the Workflow Designer.
  • The time out for each Workflow is now more easy to change, an option for time out was added to the Workflow Processor menu.
  • The saving file format is now a preference and will be remembered between instances of Huygens.

Image Stitcher & Deconvolution (E/P)
  • It is now possible to create and use Stitching templates.

MIP Renderer (E/P/L)
  • (E/P) There now is a Twin MIP renderer to quickly compare two 3D volumes.
  • More advanced contrast settings like in the (Twin) Slicer, this makes it a lot more versatile.
  • Improvements in the backend to facilitate these changes.

File Readers (All)

Minor changes
  • (E/P/L) Renderers:
    • Changed scroll-direction to zoom in and out in all the renderers to better fit zooming conventions.
  • (E/P/L) (Twin) MIP Renderer, Slicers, Render Panel and Thumbnails:
    • Addition of a "heat map" color mode.
  • (All) Nikon ND2 files:
    • On Windows and Linux the spinning disk metadata for most microscopes is now read from file.
  • (All) Image metadata:
    • New Channel Label can now be specified for every channel in an image.
    • Channel labels can be modified in the Microscopic Parameters window.
    • Channel labels are displayed in the channel selector widget.
    • Read and write support for channel labels for ICS and Huygens HDF5 files.
    • Channel labels are now read from Nikon ND2 and Imaris 5.5 HDF5 files.
  • (E/P/L) Track analyzer:
    • Plots under the intensity tab now show all tracked channels.
  • (All) GPU processing:
    • For Windows and Linux, centralize the NVIDIA cache in the Huygens installation folder. This fixes potential delays when launching Huygens.
  • (E/P/L) GUI Scaling:
    • Improve GUI scaling for various dialogs.

Bug Fixes
  • (E/P) Surfacer Renderer:
    • Fix rendering sometimes becoming unresponsive when using the high quality MIP.
  • (E/P/L) Object Analyzer:
    • Fix an issue with growing the ROI in the Z dimension.
  • (E/P) Deconvolution Wizard:
    • Fix the Decon Preview using some data from channel 0 instead of the selected channel.
  • (E/P) Colocalization Analyzer Advanced:
    • Fix an issue where Huygens could freeze after computing the colocalization coefficient while the Colocalization Analyzer was being displayed on a low resolution screen.
  • (E/P) Deconvolution Express:
    • Fix the window not being closable after the deconvolution encounters an error.
    • (E) Fix an issue where in some cases, when trying to open the Deconvolution Express, the Deconvolution wizard would open instead.
  • (E/P) Stitcher:
    • Fix an issue with memory allocation. This slightly improves operation speed and more helpful errors are shown.
  • (E/P) Bleaching Corrector:
    • Fix error messages upon unexpected closing of the bleaching corrector.
  • (E/P/L) MIP Renderer:
    • Fix improper validation of animation settings fields.
  • (E/P/L) Renderers:
    • Fix freezing/error messages in custom color selector due to improper validation of input fields.
  • (All) File readers:
    • Fix emission and excitation wavelengths sometimes not being read correctly from CZI files.


21.10.0p1

(7th of December 2021)
  • (All) MSR/OBF reader:
    • Fix for older msr images that could cause a crash when trying to find XML metadata.
  • (All) LSM reader:
    • Fix emission and excitation wavelengths not getting read in some cases.
  • (E/P/L) Object Analyzer:
    • Fix a bug introduced in 21.10p0 where some filter options would not work.
  • (All) Compute Engine:
    • Fix an issue where the img open, preOpen, and getFileType commands could not handle paths with a tilde (~) in it.
  • (E/P) PSF Distiller:
    • Fix a link to the HIW/FWHM page.
  • (E/P) Movie Maker:
    • Fix an issue where the "Surface Renderer exploration" preset would not work when preceeded by a Surface Renderer frame that uses a slicer.
  • (E/P) Deconvolution Wizard:
    • STED deconvolution:
      • Fix the wizard going astray after starting the estimation in the "Estimate psf" step.
      • The "Estimate psf" step is now also available when "Expert mode" is disabled.

21.04.0p6

(8th September 2021)
  • (All) GPU processing:
    • For Windows and Linux, centralize the NVIDIA cache in the Huygens installation folder. This fixes potential delays when launching Huygens.
  • (All) MSR/OBF reader:
    • Fix issue for Abberior v6 obf files where decompression to voxeldata failed for large chunks.

21.04.0p5

(30th August 2021)

  • (All) Histogram computation:
    • Fixed the GPU version of 1D/2D histogram for signed and unsigned integer images with voxel values smaller than 0 or larger than 32767.
  • (All) GPU Cuda code:
    • Fixed potential bugs involving out-of-bounds memory access.
  • (All) OME TIFF reader:
    • Fixed reading file series, where the Huygens image allocated was too small to contain the series.
  • (All) ICS reader:
    • Fixed handling of the parameters most recently introduced in the ICS library.
  • (All) Linux installer:
    • Fix desktop launchers occasionally showing disabled system icons instead of the Huygens products.
  • (E/P/L) Workflow processor:
    • Fixed the order of dimension conversion and deconvolution in the backend. It now correctly has the intended order of conversion before deconvolution.
  • (E/P/L) ND2 reader for Windows and Linux:
    • Improved how data coordinates are handled, this was part of the problem for previous ND2 reading issues and should fix the current issue of XY slices getting repeated over Z in some images.
  • (E/P/L) Object Analyzer:
    • (E/P) Prevent multiple Workflow Designers being opened at the same time.
    • (E/P) Performance improvements for computing colocalization statistics for many objects.
    • (E/P/L) Fix object count being off by one when watershed segmentation is used.
  • (E/P/L) Main window:
    • Fix thumbnails becoming unresponsive in some cases.
  • (E/P) Stitcher:
    • Remove superfluous question about converting tile data from channel spec packed to stacked.
  • (E/P) SFP renderer:
    • Fix issue where resizing the window before the SFP renderer is fully loaded could cause the renderer to freeze.
  • (E) Main window:
    • Made it easier to acces the Decon Express by adding a button to it in the main window.
  • (P) Main window:
    • Fix the mouseover tooltip of the GPU status button sometimes displaying outdated information.



Huygens Remote Manager 3.7


This release focuses primarily on performance and stability, but it also introduces some new features.

Detailed changes of HRM 3.7.0 are:

  • Substantially increase performance of files listing.
  • Substantially increase performance of job creation.
  • Make queue more robust against job deletion, process killing, process failure, and stalling.
  • Switch to persistent connections to the database.
  • Cache many database query results to reduce traffic.
  • Allow image channels to be assigned the restoration algorithm individually or skipped altogether.
    • This adds the possibility to use HRM as a pure batch file converter, chromatic aberration corrector, time stabilizer, etc.
  • Add an “All files” filter in the image selection step. Show by default all the contents of the raw images folder.
  • Add extreme GPU support.
  • Bug fixes.

This version of HRM works with HuCore 14.6.1-p7 or higher. For a better, faster experience we recommend using the most recent version of Huygens. Download Huygens 20.04 here.

Have fun with HRM 3.7!
(source http://www.huygens-rm.org)





For older release information see: WhatsNewArchive.