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Scientific Volume Imaging B.V.

Scientific Volume Imaging

Deconvolution - Visualization - Analysis



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.



No Tabs


What's new in Huygens 22.10


Huygens Professional, Essential, Localizer & Core

  • (L) Cluster Analyzer: new tool in the Huygens Localizer for cluster analysis of localizations:
    • Cluster the localizations in 2D or 3D using the FOCAL or DBSCAN algorithms.
    • High quality iso-surface rendering of clusters using ray tracing.
    • Measurements for volume, localization density, width, length and more of the clusters.
    • MIP rendering to use a specific channel as a reference for determining the optimal cluster parameters.
    • In-tool tutorial to get started and familiarize yourself with the main features.
    • Direct link between the rendered scene and cluster statistics table: select clusters to highlight them in both.
    • Extensive filtering options and option to export the cluster statistics to spreadsheets (.txt or .csv) or Matlab (.m).
  • (All) File readers:
    • Olympus OIR reader:
      • Full support for reading Olympus OIR files on all platforms: Windows, Linux and Mac(x86)*.
  • (All) File writers:
    • OME-TIFF:
      • Added an OME-TIFF writer to Huygens.
      • Save 5D OME-TIFF files and support writing multi-detector images using file series.
  • (E/P/L) Object Analyzer:
    • Add reported parameter for measuring the average intensity of an object.
    • Expand the list of parameters that can be used for coloring.
    • (E/P) Add an "export segmentation" button.
    • Add rows to the table for each connected component of the ROI.
  • (E/P/L) Microscopic Parameters Window:
    • Improve clarity of the parameter status symbols:
      • Verified parameters are now marked with a green checkmark.
      • Parameters that are read from file are now marked with a green dot.
  • (All) Mac M1 installer:
    • Full support for the Huygens Software suite, optimized for ARM-based M1 chips.
  • (C/E/P) Deconvolution:
    • Specific deconvolution for SoRa systems, included in the Spinning Disk option.
    • Add new microscope type for VisiTech iSIM data.
  • (E/P) Array Detector Quality Control:
    • Add a new tool for analyzing individual detector intensities and shifts for array detector images.
  • (C/P/L) Python:
    • Add functions to export Huygens image data to Python lists and vice versa.
  • (E/P/L) Help:
    • Help functions that can be found in the Huygens Core manual is now automatically opened in a Huygens Core manual.
  • (E/P) Workflow Processor:
    • Added support for batch stitching based on XML files with offsets.
  • (E/P/L) MIP rendering:
    • Improve accuracy of the rendering, especially when zoomed in.

* With the exception of ARM M1-based Macs

Minor changes
  • (E/P) Workflow Processor
    • Add option to save z mip of the image.
  • (All) File readers:
    • Tiff reader:
      • Improve support for tiff files written by imageJ, especially for large files (BigTiff).
      • Add support for reading jpeg encoded tiff files on Windows.
      • Add support for reading deflate compressed tiff files on Windows.
    • OME-TIFF reader:
      • Improved reading of different OME-TIFF file configurations, including files written by Slidebook.
      • Improved reading of metadata.
    • Olympus VSI:
      • Improved reading of metadata.
    • Nikon ND2:
      • Improved feedback after failing to read a file.
      • Improved reading of metadata.
  • (All) File writers:
    • Tiff: Add support for writing multi-detector images.
  • (E/P/L) User interface:
    • Add sliders to make it easier to navigate through channels, time frames and detectors in the histogram tab in the main window.
    • Added image dimension in the sub-image selection window.
  • (E/P/L) Cropper:
    • Improve automatic cropping for array detector images.
  • (E/P/L) Chromatic Aberration Corrector:
    • Automatically choose the initial setting for the reference channel.

  • Huygens Nyquist Calculator (on svi.nl)
    • Added the new Sora and VT-iSIM microscope types.
    • Added Zeiss Airyscan 2 Sheppard Rings detector model for array detector microscopes.
    • Sanitize and warn for lens immersion refractive index and numerical aperature mismatches.
    • Warn for an invalid combination of wavelengths and excitation photon count.

Bugfixes
  • (E/P/L) Microscopic Parameters Window:
    • (Windows) Fix some options not being visible.
  • (All) Gpu processing:
    • Fix an issue where GPU processing would not get enabled when switching from a license that does not allow GPU processing to one that does.
  • (E/P) (Twin) Mip Renderer:
    • Fix an issue where the depth rendering would not work for images with more than 4 channels.
  • (E/P/L) Preferences
    • Fix an issue where thread restrictions were not applied correctly in some cases.
  • (All) File readers:
    • OME-XML reader:
      • Fix reading in files upside-down, i.e. with an inverted Y-axis.
      • Enable reading OME-XML files written in the the 2016_06 schema.
    • OME-TIFF reader:
      • Fix the -series auto option of img_open not recognizing a series for files with .ome.tif(f) extension.
    • Abberior OBF:
      • Fix regression where some older obf files with compression were not read.
  • (All) File Writers:
    • OME-XML writer:
      • Fixed issue where files were saved upside-down, i.e. with an inverted Y-axis.
  • (E/P) Bleaching Corrector:
    • Fix an issue where access was wrongly blocked when only multi-photon microscopes were licensed.
  • (L) Table Export window:
    • The 'The name of the table to create' entry now actually becomes the name of the opened table.


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.


22.10.0p5

(1st of March 2023)
  • (All) File reader:
    • LIF: Fix only reading in the first sub image for FLIM Tau STED data.
    • OBF/MSR: Fix memory leak that occurred for tiled datasets when parsing OME-XML metadata in OBF files.
    • OME-TIFF: Fix the offset of a multi-file series for files exported by VisiView.
    • OME-TIFF: Fix an issue where only a single z-slice was read in from a z-stack for files exported by ImSpector.
    • OME-TIFF: Fix for rare case where the ome-tiff reader could hang.
    • OME: Fix memory leak that occurred when reading in OME-TIFF or OME-XML files.
    • (C) VSI / ND2: improve reading metadata for spinning disk images.
  • (L) Cluster Analyzer:
    • Fix the threshold (slider) not correctly initializing to 0.5 for all channels except the first one.
    • Fix the average intensity parameter not being reported.
  • (E/P) Decon Wizard:
    • Fix an issue where the iteration count used for QMLE was not updated properly when editing the acuity or SNR.
  • (E/P/L) Object Analyzer:
    • Fix an issue causing distance to surface computions to take much longer than needed.
    • Fix an issue where formerly removed objects could not be highlighted anymore after reloading the data.

22.10.0p4

(7th of February 2023)
  • (All) File writer:
    • TIFF: fixed an issue where multi-directory tiffs/tiffs contain all z-slices in a single file could overwrite existing files without a warning.
    • TIFF: no longer remove the last number in the filename when saving a tiff series, if the number is not clearly a slice, time frame, channel or detector counter.
  • (E/P/L) Object Analyzer:
    • Fix an error when selecting all objects as anchors.
    • Fix an error when changing the threshold value in the MIP segmentation group.
  • (L) Cluster Analyzer:
    • Fix distance configured to be reported on-screen not being plotted for 2D data.
  • (All) Deconvolution:
    • GMLE: fixed a resource leak that could cause deconvolution to fail with an error: "Variable overflow detected during execution"
  • MacOS Ventura:
    • (E/P/L) The release of macOS Ventura introduced a regression that caused applications handled by XQuartz (like Huygens) to get unexpectedly minimized in some cases. This patch adds some workarounds to mitigate this, but some issues might persist.

22.10.0p3

(4th of January 2023)
  • (All) File writer:
    • OME-TIFF: fix regression, since 22.10.0p1, writing the companion.ome file at the wrong location.
    • OME-TIFF: fix issue with writing (and reading) multi-detector images containing multiple slices/frames or/and channels.
  • (All) File reader:
    • ND2: fixed an issue where for some SoRa images the pinhole diameter was not read correctly.
  • MacOS:
    • (E/P/L) Extend the fix for font related crashes that was first deployed in 22.10.0p2. In particular, these type of crashes should now also be fixed on macOS Ventura.

22.10.0p2

(13th of December 2022)
  • (All) License manager:
    • Fix regression where errors would not be displayed when adding a wrong license to the license manager.
  • (All) GPU Processing:
    • Improve description of steps to take when CUDA Toolkit is not found.
  • (E/P/L) User Interface:
  • (E/P/L) Object Analyzer:
    • Fix an issue where pressing "Reload original data" would not reinstate objects in all time frames and/or detectors.
  • (E/P) Mip Renderer:
    • Fix an issue where the Mip Renderer could crash when rendering a very large image in High Quality mode.
  • MacOS:
    • (E/P/L) Fix an issue where Huygens could crash when a specific font library would fail.

22.10.0p1

(30th of November 2022)
  • (All) File reader:
    • CZI: fix crash on Windows when reading JPEG-XR compressed data.
    • OME-XML: fix a regression breaking the OME-XML reader since the 22.10 release.
  • (All) File writer:
    • OME-TIFF: fix OME-TIFF writer not correctly handling file paths longer than 128 characters.
    • OME-XML: fix a regression breaking the OME-XML writer since the 22.10 release.
  • (All) GPU Processing:
    • Fix Huygens crashing when loading the CUDA library fails in an early stage.
  • (E/P) Decon Express:
    • Fix an issue where the result image could have incorrect scaling when operating under low memory conditions.
  • (E/P/L) Object Analyzer:
    • Fix an issue where some operations (such as deselecting all anchors) were not applied to all time frames and/or detectors.
  • (E/P/L) User interface:
    • Improvements for the user interface scaling that can be set in the preferences.
  • (E/P) Ortho Slicer:
    • Fix a regression where xz- and yz-slicers were initialized at the wrong position.


22.04.0p7

(19th of October 2022)
  • (All) File reader:
    • OME-TIFF: fix some .companion.ome files not being read correctly on Windows.
    • CZI: improve estimation of backprojected pinhole sizes.
    • VSI: Fix a rare issue where the image data would appear slanted when opened in Huygens.
  • (E/P) Deconvolution Express:
    • Fix an issue where access was wrongly blocked when only multi-photon microscopes were licensed.
  • (E/P/L) Object Analyzer (Basic):
    • Fix setting the parameters to be displayed on scene when loading a predefined preset from the preferences.
  • (E/P/L) User interface:
    • Various improvements for the user interface scaling that can be set in the preferences.


22.04.0p6

(20th of September 2022)
  • (All) Deconvolution, Parameter Editor and related Huygens Tcl commands:
    • Add new microscope type VT-iSIM for Visitech iSIM data.
  • (All) File reader:
    • CZI: fix an issue where pinhole sizes were estimated incorrectly for some multi-channel images.
  • (E/P) Deconvolution Wizard.
    • Fix a rare crash during deconvolution of brightfield images.
  • (E/P/L) Cropper:
    • Fix an issue where the cropper could get stuck when the GUI scaling was set to a value slightly higher than 1.
  • (L) Table Export window:
    • Fix an issue where selecting one of "Apply a 1/2 pixel shift to the XY origin" and "Flip the Y axis" always applied both.
  • (L) Main menu:
    • Fix the option to shift an image in 3D under Tools->Shift Image.

22.04.0p5

(23rd of August 2022)
  • (E/P/L) Object Analyzer (Basic):
    • Fixed an issue where the coloring based on the analysis parameters resets when changing the transparency depth.
  • (E/P) Stitcher:
    • Fix for errors that could happen when loading multiple sets of tiles from a single container file.
  • (E/P) Workflow processor:
    • Fixed an issue with the thumbnail previews on Windows not showing up.
  • (All) GPU Processing:
    • Allow the GeForce RTX 3090 Ti card to be used with the large GPU license option.
  • (All) Windows:
    • Fix for issue that showed a warning* that would shut down Huygens if closed.
      *OMP: Warning #... Cannot not determine machine load balance - Using KMP_DYNAMIC_MODE...


22.04.0p4

(3rd of August 2022)
  • (E/P) Deconvolution Wizard:
    • Fix a rare crash of the Wizard in the automatic background estimation stage.
    • Fix a bug where the QMLE algorithm for widefield and spim images would always deconvolve using the default settings.
  • (E/P) Movie Maker:
    • Fix an error pop-up when switching from the Surface Renderer to another renderer.
    • Fix an issue where the Movie Maker could no longer start a new renderer after the launch of one of them was cancelled.
  • (E/P/L) Object Analyzer (Basic):
    • Fixed an issue where statistics were not reported for some objects when both the Gaussian Filter as well as the Minimum Object Size option were used.
  • (E/P/L) User Interface:
    • Fix DPI scaling being accidentally applied twice on startup.
    • Limit resizing of the Histogram Tab so that it cannot be hidden, or completely overlap the thumbnail panel.
  • (E/P/L) Workflow Processor:
    • Fix an error with thumbnail creation that could occur when there was a space in the path to the output directory.
  • (All) OME-TIFF reader:
    • Improve reading the object settings form SlideBook images.
  • (All) OBF/MSR reader:
    • For STED channels, the STED mode for Abberior files is now initialized to STEDYCON (Facility/Expert).
  • (E/P/L) MIP Renderings:
    • Introduction of a hot pixel corrected display range.

22.04.0p3

(5th of July 2022)
  • (E/P) Deconvolution Wizard:
    • Fix a regression introduced in the previous patch (22.04.0p2) where the Deconvolution Wizard would crash after opening the Deconvolution Preview.
  • (All) GPU Processing:
    • Allow the GeForce RTX 3080 12GB card to be used with the large GPU license option.

22.04.0p2

(29th of June 2022)

  • (E/P) Decon Express:
    • Fix an issue where the "Adjust acuity" stage would not start for some images.
  • (E/P) Deconvolution Wizard:
    • Remove unnecessary warning about the backprojected pinhole being too large for array detector images.
  • (E/P/L) Hot & Cold pixel remover:
    • Fix an issue where the display option to show both the image as well as the hot/cold pixels did not work since the 22.04 release.
  • (E/P/L) Workflow Processor:
    • Fix a rare issue where images containing identically named subimages were not opened correctly.
  • (All) File Readers:
    • Metamorph STK: Sampling distances and the emission wavelength are now read from file.
    • Metamorph ND 2.0: Z sampling is now always read from file.
    • OBF Facility Line: Fix issue where reading tiles ended up in detector-dimension due to unexpected DimensionOrder XYZCT.
  • (E/P/L) Look-Up Table (LUT) Editor:
    • UI update for more ergonomic use.
    • LUTs are no longer forced to start at black.
    • LUT changes now always apply to the currently edited channel, with the option of applying to all other channels.
    • Various bugfixes.

22.04.0p1

(2th of June 2022)

  • (All) Czi file reader:
    • Fix regression introduced in 21.10.1 where the backprojected pinhole size was not computed correctly when no physical pinhole size was present in the metadata.
  • (E/P) Surface Renderer:
    • Fix regression introduced in 22.04 where the slicer option would only display channel 0.
  • (E/P) Deconvolution Wizard:
    • Fix regression introduced in 21.10.1 where a measured PSF would not be saved properly in templates.
  • (E/P) Stitcher:
    • Fix regression introduced in 21.10.1 causing problems with using .xml files for stitching.
    • Fix regression introduced in 21.10.1 causing deconvolution always being skipped.
  • (L) Tables:
    • Fix an issue where the values of the FWHM-X(FWHM-Y) where stored in the FWHM-Y(FWHM-X) column. This does not change the z-position of the localizations for 3D SMLM.



Huygens Remote Manager 3.8


We are happy to announce the immediate availability of HRM 3.8.0!

This release adds several new functionalities and makes a few changes that require a slight update in the minimum required versions of PHP and HuCore for the first time in several years:

New minimum required versions for HRM 3.8 are now PHP 7.2 and HuCore 21.10.1

Also, please notice that there was a simplification in the configuration files. See the upgrade instructions for more details (estimated time for upgrading ~20 minutes).
Changelog

New features and changes in HRM 3.8.0 are:

  • Added Hot Pixel Remover as optional pre-processing step
  • Added new Acuity restoration parameter
  • Added support for Olympus VSI files
  • Added option to disable bleaching correction
  • Added Python pip package for installing the HRM-OMERO connector very easily
  • Enhanced usability in OMERO Connector
  • Updated list of instruments in back-projected pinhole calculator
  • Merged server and client configuration files into one
  • Extended and updated documentation
  • Several fixes and usability enhancements

Hope you will enjoy the new HRM 3.8.0 release!

You can download HRM 3.8.0 from the official download page: http://huygens-rm.org/wp/?page_id=11.

You can also test our *experimental* new HRM installer!
(source http://www.huygens-rm.org)





For older release information see: WhatsNewArchive.