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 20.10

Huygens Everywhere & new style Huygens Floating licenses

  • New user portal for license administration. Log in with your svi.nl account. Add/remove users to/from your licenses. Set the maximum allowed concurrency on a per-user basis.
  • Get your licenses and subscriptions at the SVI webshop.

Huygens Professional & Essential

Image Restoration
  • Airyscan 2: Sheppard 4-ring data now supported. If available, 32 detector raw data from Airyscan 2 is also supported.
  • Brightfield: add 'ctm' algorithm to Workflow Processor, Deconvolution Wizard, Decon Express, and Batch Feeder for transmitted light images. The algorithm takes care of intensity inversion, PSF calculation, background estimation, bricking, etc. Available for CPUs and GPUs.

Workflow Processor
  • Replaces the Batch Processor tool in Huygens Essential, Professional and Localizer.
  • Shows previews of the result image during and after processing. These previews allow you to quickly access the results in different Huygens tools.
  • Create complete image processing sequences with the new Workflow Processor. In this Processor the various stages constituting a Workflow Task are shown as an interactive block diagram. Drag and drop stages to create your Workflow.
  • List of operations:
    • Conversion of image dimensions, cropping (both with templates and on auto mode), correction of hot/cold pixels, stabilization of Z stacks, baseline adjustment, deconvolution (including bleaching correction and background subtraction), stabilization of time series, correction of chromatic aberrations, correction of Z drift.
  • Additional features:
    • The saving directory and format can be set for individual tasks
    • Conversion of file formats in batch mode.

Huygens Python scripting
  • Added Python scripting capabilities to Huygens Professional, Huygens Localizer, and Huygens Core
  • Allows manipulation of images and SMLM localization tables with the full set of operations that are also available in Tcl.
  • Scripting can be performed directly in the Huygens interface or by using .py scripts loaded from the command line.
  • Additional Python modules can be imported for even more options.
  • Note: currently supported on Linux and Windows.

Image Slicer
  • Renewed Image Slicer.
  • Includes line plotting, movies, MIP and SUM projection modes, overlays, exports, and more.
  • Improved contrast and color control.
  • Improved linking of slice position, zoom, color and contrast settings with other slicers.
  • Includes a 'clone' option for easy, fast replication of the slicer instance.

Minor changes
  • (All) GPU support
    • CUDA versions 7.x no longer supported.
  • (E/P) Object Analyzer
    • Renamed graphics pipes into segmentation groups and improved location of channel selection.
    • Watershed segmentation and garbage volume entry are now easily accessible.
  • (E/P) Stitcher:
    • Clearer feedback on the progress of loading tiles.
    • One single open button for all types of files and patterns. This replaces drag&drop option introduced in 20.04.0p3.
    • Make it optional to visualize the tile guides and numbers.
  • (E/P) Cropper:
    • Add support for templates.
  • (E/P) Deconvolution Wizard:
    • Add visualization controls (brightness, contrast, colors, zoom, ..)
  • (E/P) Batch Express:
    • Renamed as Batch Feeder.

Bug Fixes

  • (All) CZI reader:
    • Fix potential shift in excitation wavelengths.
  • (All) TIFF reader/writer:
    • Fix performance regression on Windows.
  • (E/P) Cropping tool:
    • Fixed an issue with the preview.
    • Fixed an issue with the placement of the MIP sliders after resizing the window.
  • (E/P) Fuser:
    • Made finding the axial shift along the main axis of rotation more robust.
  • (E/P) Object analyzer and hybrid renderer:
    • Changed the definition of the seed level when watershed segmentation is used. The seed level now refers to the intensity level that must be reached in the original image, rather than the Gauss-filtered image. This makes the results before and after watershed segmentation more comparable and fixes issues with small objects disappearing when using watershed segmentation.
  • (E/P) Stitcher:
    • Fix excessive memory allocation when working with images of unsigned integer type.


(8th April 2021)
  • (All) Huygens Everywhere:
    • Indicate the progress of contacting the servers in the Login window.
  • (All) GPU Processing:
    • Fix issue with loading the enabled devices from the preferences.
  • (All) Updates:
    • Fix notification when the GDPR message has not yet been accepted.


(8th March 2021)
  • (All) VSI reader:
    • Fix for loading the first sub image from Tcl scripts without specifying the sub image index.
  • (All) CZI reader:
    • Don't map channels with unspecified microscope types.
  • (All) HDF5 reader:
    • Significantly faster on Windows.
  • (All) MSR/OBF reader:
    • Significantly faster on Windows.
  • (All) GPU Processing:
    • Accept other names for the GTX 1650 card.
    • Implement missing sub cases of the image histogram 'hist' operation.
    • Implement the 'roiStat' operation.
  • (All) Deconvolution:
    • Fix small memory leak in CMLE.
  • (E/P/L) Huygens Everywhere:
    • Use port 9118 on the second server from the list. This should help in making it work with proxy servers and some firewalls.
    • Don't throw an error if there are multiple attempts to create the login window.
    • Fix client hanging on broken communication.
  • (P/L/C) GUI:
    • Fix ocassional error message on Huygens shutdown caused by memory widget updates after GUI destruction.
  • (E/P) Stitcher:
    • The flat field and dark frame images used for manual vignetting correction can now have any number of planes and channels.
  • (E/P) Movie Maker:
    • Fix errors in some presets.
  • (E/P) PSF Distiller:
    • More accurate normalization of multi channel PSFs.
  • (E/P) Workflow Processor:
    • Better handling of TIFF types for saving data.
  • (E/P) Object Tracker:
    • Fix rendered image and overlay when drawing ROIs.
    • Add an option to import ROIs from the main window.
    • Make the Object Tracker available in Huygens Localizer.
  • (P) Operations Window:
    • Save the proper SNR value and tag to deconvolution templates.


(January 27th 2021)
  • (All) Compute Engine:
    • Fix an issue where repeated use of some modules during one session could cause "Cannot handle more strings" errors.
  • (All) VSI reader:
    • Fix for Huygens crashing on opening images with missing tiles or aborted time series.
    • Fix for missing planes in files with very large pyramids and Z dimension > 1.
  • (All) CZI reader:
    • Fix regression for files reporting custom but empty compression schemes.
  • (All) ND reader:
    • Fix for loading the first sub image from Tcl scripts without specifying the sub image index.
  • (All) OBF/MSR reader:
    • Fix for cases where the meta data is split across multiple annotation nodes.
  • (All) GPU support:
    • Fix for theoretical, multichannel PSFs with spherical aberration.


(January 12th 2021)
  • (All) GPU support:
    • Raise the limit for GPU memory on 'Small' GPU cards from 3 to 6 GB.
  • (All) OME-TIFF reader:
    • Fix potential crash on Slidebook images.
  • (All) Compute Engine:
    • Improve event handling. Solve warning about 'too many events in buffer'.
  • (All) VSI reader:
    • Add support for pyramid RGB files.
  • (All) LIF reader:
    • Fix interpretation of meta data for non standard "," as decimal point indicator.
    • Improve reading of meta data for non-descanned detector channels.
  • (All) MSR reader:
    • Fix potential crash on images with no meta data.
  • (E/P/L) Object Analyzer:
    • The user interface (UI) has been updated:
      • The old reference cube has been replaced with a new orientation indicator, which is shown in the bottom-right corner of the canvas.
      • Settings for garbage volume and watershed segmentation are now shown beneath the histogram.
      • Settings for visualization (transparency, brightness, hue) have been moved to a separate "Visualization" tab.
      • Various other buttons in the main window have been moved to a new location.
      • The old "Conditions" row in the statistics table has been split into two rows, "Conditions" and "Findings".
    • Advanced only (E/P):
      • The functionality for creating your own experiment presets (user presets) has been expanded. The preset selection window now shows three available user presets by default, and user presets can be edited from within this window.
      • When creating a 360° movie, the renderer will now use the segmentation conditions you specified.
  • (E/P) Decon Express:
    • Fix potential abrupt termination on Array Detector images.


(15th December 2020)
  • (All) GPU support:
    • Add support for the 'GeForce GTX 1660 Super' card without a GPU license.
    • Disable the GPU system when any module (ptx file) fails to load, preventing error messages about NULL modules later on.
    • Check for the cards with Compute Capability between 3.0 and 3.5 that are no longer supported by Huygens 20.10. Give a proper error message instead of letting GPU operations fail later on.
  • (All) Array Detector Deconvolution:
    • Improve results when on GPU mode.
  • (All) OME-TIFF reader:
    • Fix error for tiled files containing misleading meta data about dependencies with other files.
  • (E/P/C) Batch Processing:
    • Fix propagation of quality thresholds for GMLE.
  • (E/P) Chromatic Aberration Corrector:
    • Improve matching template channels to image channels for microscope types 'Array Detector' and 'Rescan'.
    • Fix potential issue when loading two or more different templates in one tool instance.
  • (E/P) Object Analyzer:
    • Fix reported colocalization volume and sum when on GPU mode.
  • (E/P) Image Stitcher:
    • Fix rerouting of some CZI files containing tiles which did not prompt questions about loading in the Stitcher.
  • (E/P) Slicers:
    • Fix occasional issue with limiting zoom factors.


(25th November 2020)

  • (All) GPU support:
    • Remove inaccurate message "Processing on CPU" from CMLE while Huygens was using the GPU.
    • Update the tooltip text on the GPU status icon in Huygens Professional when the GPU has been successfully initialized.
    • Warn about a graphics driver that is too old for the Cuda Toolkit version when the Cuda Toolkit version is 9 or lower.
  • (All) CZI Reader:
    • Fix potential memory overflows that could lead to a crash.
  • (E/P) Image Segmentation:
    • Fix interpretation of the seed value in watershed segmentation.
  • (E/P) Chromatic Aberration Corrector:
    • Fix glitch in template selection panel.
  • (E/P) Deconvolution Wizard & Brightfield Deconvolution:
    • Fix for when brightfield channels are skipped.
  • (E/P) Image Renderers (MIP, SFP, Surface):
    • Faster for large images. Added an option to the Huygens Preferences to dynamically adapt the image size.
  • (E/P) Image Thumbnails:
    • Fix slider style.
    • Now render faster for large images.
  • (E/P) SFP Renderer:
    • Fix incorrect negative values for tilt and twist.
  • (E/P) Workflow Processor:
    • Add an option to select all images in a folder.
    • Switch to other presets and back without losing the edited parameters.
    • A clearer channel selection in the Deconvolution Template editor.
    • Fix potential empty thumbnails on Windows.
  • (P) Main Menu:
    • Fix 'Workflow Processor' entry which only got enabled on selecting an image.

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.