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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 22.04

Huygens Professional, Essential, Localizer & Core

  • (E/P/L) Object Analyzer: Full version available in Professional and Essential, basic version available in Localizer
    • New coloring options: it is now possible to color the objects based on some of their properties. For instance objects with the same parent can be given the same color.
    • Added tools for cluster analysis. In the Object Analyzer it is now possible to cluster objects with the DBSCAN algorithm. The resulting clustering can be visualized in the rendering, and the cluster ID of each object will be saved in the table. Furthermore, some properties of the clusters themselves will also be reported.
    • The new reported parameter ObjectCnt can be used to count the number of objects inside the ROI or in a cluster.
    • Added the "Quick analysis" preset that only reports the basic parameters.
    • The watershed segmentation algorithm will now create larger segments overall, and a new parameter was added to better control how much objects will be split up by the watershed algorithm.
    • The table now has a "customize table" button where one can control which rows need to be displayed.
    • The Object Analyzer now remembers which objects were merged or removed after switching channels, time frames or detectors.
    • Workflow Designer (E/P): add support for the newly added segmentation and coloring options.
  • (E/P/L) Look-Up Table (LUT) Editor:
    • Addition of a new look-up table (LUT) editor to the (Twin) Slicer and (Twin) MIP renderer.
    • Color images using custom-made look-up tables mapping image intensities to colors.
    • Use the LUT tab in renderers to load, view and edit Huygens CSV-based LUTs and .lut files.
    • Define look-up tables for the channels of your image and interactively view the effects in the renderers.
    • Adjust your LUT with ease using the graph or wedge-based representations.
    • Add smooth color transitions (i.e. color gradients) to specific selections of look-up table elements.
  • (E/P/L) Object Tracker & Track Analyzer:
    • Add spiderplot in Positions tab to see all object's paths with respect to their origin.

Minor changes
  • (All) File readers:
    • OME-TIFF: Improve reading files using a header only in the first .ome.tiff or companion file to store the OME-XML metadata.
  • (P) File writers:
    • TIFF: when using the contrast stretch mode the scaling factors are now reported in the task report.
  • (All) GPU Processing:
    • Added GPU support for a number of 2D image rendering commands.
  • (E/P) Deconvolution Express and the Deconvolution Wizard:
    • Improved interactivity.
  • (All) Deconvolution templates:
    • Added the possibility to "Remove" a channel instead of skipping it if you don't want to process it.
  • (E/P/L) (Twin) Slicer and (Twin) MIP renderer:
    • When exporting an image, it is now possible to set the dimensions of the exported image.
  • (E/P) Surface Renderer and (E/P/L) Object Analyzer:
    • The minimum size of an object can now be specified in either micron² or micron³ or in the number of voxels.
    • It is now possible to apply a Gaussian filter (smoothing) before segmenting the image (previously this was only possible when watershed segmentation was used).
  • (E/P/L) License Window:
    • Added an overview with the currently activated license options, including links to relevant web pages.

Bugfixes
  • (E/P) Deconvolution Express and the Deconvolution Wizard:
    • Fix an issue with the deconvolution preview for superY and superXY deconvolution with Airyscan images.
  • (E/P/L) Object Analyzer:
    • Fixed an issue where sorting the table columns would not work in some cases.
  • (E/P) Object Stabilizer:
    • Improved handling of time series for the light-sheet deskewing option
  • (P) Operations Window::
    • Fixed the "Analysis -> Plot line profile" operation.
  • (E/P/L) User Interface:
    • On Windows show a separator icon to indicate the possiblity of dragging to change the size of a window.
  • (E/P) Interactive Fuser & Decon:
    • Fix incorrect memory estimation on opening a file when not all sub-images were selected for fusion, resulting in a "The file is too big to load" error.


What's new in Huygens 21.10.1 ('Christmas Special')

Huygens Professional, Essential, Localizer & Core


  • (E/P/L) Chromatic Aberration Corrector
    • New estimation methods that can correct for 3-D rotation, expansion/shrinking and radial non-linear distortions in addition to a 3-D shift were added to the existing Chromatic Aberration Correction Window.
    • A new Chromatic Aberration Correction Wizard was added with more explanation, guidance on which estimation method to choose, as well as more flexibility in enabling and disabling separate components of the aberration. This tool contains a visualization of the per-channel aberration in a 3-D wireframe view.
    • Handling in templates of the new components/types of aberration that can now be corrected for.
  • (E/P/L) Object Analyzer
    • Changes to the interface of the right column. In particular the channel selector now also shows the channel label.
    • Improve contrast of objects after discard or merge operations.
  • (E/P) Surface Renderer
    • Changes to the interface of the right column. In particular the channel selector now also shows the channel label, and the segmentation settings are now shown for only one group at a time.
  • (E/P) Deconvolution Wizard
    • The SNR is now estimated automatically. It can still be overridden if preferred.
    • Add a slider for the acuity (sharpness) of the result.
    • Minor changes to the organization of the wizard stages.
  • (All) File readers
    • CZI: Improve estimation of backprojected pinhole sizes.
    • OME-TIFF: Improve reading in Micro-Manager exported files.
    • OBF: Reading of STED 3D parameter added.
  • (All) File Series Tool:
    • Added option for reading array detector images from a series of images.
  • (E/P) Bleaching Corrector
    • It is now possible to correct images that contain one or more channels that are unsuitable for correction (on those channels no correction will be performed).
  • (E/P) Object Stabilizer
    • Add plot options to the displacement graphs so data and plots can be exported.
  • (E/P/L) 3D Renderers:
    • Change zooming and rotating so that it no longer occurs relative to the center of the image, but to the center of the screen.
    • Change panning so that it no longer occurs relative to the screen, but to the image.

Minor Changes

Bugfixes
  • (E/P/L) MIP Renderer:
    • Fix rendering issue causing glitchy full rendering in timeseries.
  • (E/P/L) Object Analyzer
    • Fix for the ROI shift function which had become unusable.
    • Fix an issue introduced in the 21.10.1 beta where the hue range was not applied correctly in some cases.
  • (E/P) Bleaching Corrector
    • Fix for a number of table-related bugs when only correcting a range of z-planes and frames.
  • (E/P/L) Multiple renderers
    • (Windows) Fix for "Domain error" pop-up that sometimes was shown when panning.
  • (E/P) Object Stabilizer:
    • Fix an issue where the Object Stabilizer could crash when going back and forth between different stages.
  • (E/P) Deconvolution Express:
    • Fix an issue introduced in the 21.10.1 beta where the ROI deconvolution would fail for brightfield images.
    • Fix an issue introduced in the 21.10.1 beta where the Express deconvolution would fail for Zeiss Airyscan2 Rings images.
  • (E/P) Deconvolution Wizard
    • Fix an issue introduced in the 21.10.1 beta where the airyscan reduction mode could get stuck on "auto".


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.


21.10.1p2

(16th of March 2022)

  • (E/P) Deconvolution Wizard:
    • Fix an issue where the inversion of brightfield channels in a multi-channel image did not work correctly in some cases.
  • (E/P/L) Object Analyzer:
    • Workflow Designer (E/P): Fix the "Experiment report" step not getting verified sometimes.
    • Fix table tooltips not working correctly when hovering over a conditions row while a column is selected.
  • (E/P) Fusion Wizard:
    • Fixed an issue that prevented deconvolution templates from working in the Fusion Wizard.
  • (E) Abberior Feeder:
    • Add abberior feeder toggle to the import options in the File-menu.
  • (All) Non-graphical start-up:
    • Fixed a regression that blocked LASX HyVolution from working.

21.10.1p1

(8th of February 2022)
  • (E/P) Deconvolution Wizard:
    • Added an editor for the numerical value of the acuity.
  • (E/P) Deconvolution Express:
    • Fix regression where Airyscan images acquired with Fast-mode sometimes contained empty regions after deconvolution.
  • (E/P/L) Object Analyzer:
    • Fix an issue where merging a very large number of objects could cause errors.
    • Fix computing the distance to anchor surface for the ROI, if the anchors are analyzed before the ROI.
  • (L) Chromatic Aberration Corrector Wizard:
    • Fix the quick launch button of the Chromatic Aberration Corrector.
    • Fix an issue where some of the buttons for opening other tools were not working correctly in the Localizer.
    • Improved the behavior when closing the window while calculations are busy.
  • (E/P) Object Stabilizer:
    • Fix an issue where model-based stabilization could produce outliers with large incorrect shifts when the GPU was enabled.
  • (All) LIF file reader:
    • Fix bug when reading metadata of light sheet lif files, which caused the microscopic parameters to not be applied.
  • (E/P) Microscopic parameter editor:
    • No longer show the TIRF and SMLM 3D microscope types. These types were only intended for Localizer and could cause various issues in Essential and Professional.


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.



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, which you can download from here.

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





For older release information see: WhatsNewArchive.