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 21.04

Huygens Professional & Essential

PSF Distiller
  • Support for array detector images (Airyscan I & II, SPAD, etc).
    • Distill array detector PSFs from bead images.
    • Obtain even better deconvolution results on array detector images by using distilled PSFs.

  • FWHM Estimator:
    • Automatically find the FWHMs of the distilled PSFs and compare them with their theoretical counterparts.
    • Inspect the lateral and axial FWHMs of each independent channel and detector.
    • Export the FWHM data to .csv or .txt files.

Deconvolution Express
  • Improved interactivity and contrast handling
  • Automatic selection of an interesting region of interest

Image Stitcher & Deconvolution
  • New option to prefilter image intensities exclusively during the optimization stage.
    • This is useful for reducing the effect of hot/cold pixels in the final tile positions.
  • New option to skip the optimization step for directly stitching the data with the input tile offsets.
  • The flat field and dark frame images used for manual vignetting correction can now have any number of planes and channels.
  • Support for Abberior Facility Line .obf files.

Object Analyzer Advanced
  • Create analysis workflows with the new Workflow Designer. In the Workflow Designer the various tasks constituting a Workflow are shown as an interactive block diagram. Drag and drop tasks to create a Workflow.
  • Load/save workflows as templates. Reproduce the experiment and image analysis with these workflow templates.
  • List of operations:
    • Set and customize segmentation groups, Regions Of Interest (ROI), visualization parameters, object anchors, parameter filters, general analysis options, experiment reports, table exports.
  • Use predefined Workflows for some common experiments, like measuring geometric properties of objects, colocalization analysis, or computing total volume.

Workflow Processor
  • New task for configuring file series:
    • Selecting a file from a series loads the File Series tool for further customization of the channels, time frames, and slices.
    • Selecting a container file (e.g. .czi, .lif) allows for further inspection and selection of its contents (sub images).
  • Renamed Task Designer as Workflow Designer.
  • New option to edit existing workflows.

Minor changes
  • (All) Huygens Everywhere
    • Optimize server connection.
  • (All) Abberior OBF files:
    • Support for reading of v6 obf files.
    • Better handling of Facility Line meta data.
  • (All) Nikon ND2 files:
    • Enhanced support for reading nd2 files on Windows and Linux.
  • (All) CZI reader:
    • Rename tag 'AirySheppardLines' as 'MergedAiryFastMode' for Airyscan2 fast mode images.
  • (E/P) SFP/MIP/Surface renderer
    • Add Orientation indicator to the canvas.
  • (E/P) Object Analyzer Advanced
    • The "Analyze ROI volume" option now reports the segmentation conditions and object count in the table.

Bug Fixes
  • (All) GPU processing:
    • Fix "Out of memory" errors on some Windows systems which could occur when another application was using GPU memory simultaneously.
  • (All) Leica lif files:
    • Fixed regression where sometimes STED parameters were not fully read in.
  • (E/P) Object Analyzer Advanced
    • Removed the dysfunctional option to set anchors by filtering all time frames or detectors.


(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.


(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.


(19th July 2021)

  • (All) CMLE deconvolution:
    • Increase the estimated amount of memory needed. This can result in more bricks being used. It prevents CPU/GPU data migration from slowing down the deconvolution.
  • (All) Deconvolution on Mac OSX:
    • Let the deconvolution result be in floating-point data if the amount of memory allows it, in the same cases as on Windows. This prevents loss of precision by unnecessary rounding to integer-typed results.
  • (E/P/L) User interface
    • Fix an issue with using the mouse wheel to scroll on Windows.
  • (E/P/L) PSF Distiller:
    • Fix excessive memory usage and computation that could also lead to a crash, when multiple beads are accumulated on Windows without GPU.
  • (E/P/L) Object Analyzer:
    • Fix the statistics pop-up sometimes not displaying analysis statistics correctly on Windows.
  • (E/P/L) Track analyzer:
    • Fix not being able to complete a drawn boundary with double click.
  • (E/P/L) ND2 reader for Linux and Windows:
    • Fix an issue where the Z planes and time frames got mixed up.
  • (E/P/L) Workflow Processor:
    • Fix an issue when saving tiffs with long names. It will now truncate long names.
  • (E/P/L) Slicer:
    • Fix memory leak when the same image was plotted twice.
    • Added the option to disable automatic generation of a new slicer to show the line profile plots in.
  • (E/P/L) Default metadata:
    • The default emission wavelenghts for 3-channel images without metadata have changed to a red, green and blue wavelength. This makes actual RGB images recognizable and uses wavelengths of commonly used fluorophores.
  • (E/P) Image Stitcher:
    • Fix regression introduced in the previous patch in the form of an occasional message 'missing value to go with key'. This occurs to some tiles missing both proper meta data and name patterns indicating the offsets.


(28th June 2021)

  • (All) Huygens Everywhere:
    • Fix the use of svi.nl passwords containing special characters.
  • (All) Cropper / Compute Engine:
    • Automatic cropping now crops the axial direction less aggressively for widefield and brightfield images.
  • (All) GPU support in Windows:
    • Fix regression in version 21.04 that resulted in poor GPU performance.
  • (All) MSR/OBF reader:
    • Fix memory leak.
  • (All) ND2 reader:
    • Fix swapped Z/T dimensions in some images.
  • (All) Compute Engine:
    • Fix the watershed command sometimes failing for images that segment into a large number of objects.
  • (E/P/L) Twin Slicer:
    • Fix contrast not being applied correctly when the contrast option "Custom compression" is selected for the first time.
  • (E/P/L) Object Analyzer:
    • Fix object count and anchor count not being displayed after clearing the table.
    • Fix an issue where under rare circumstances clicking an object would not trigger an analysis of the object.
  • (E/P) Deconvolution Express:
    • Fix for the error message 'can't read "orgSizeS": no such variable'.
    • Fix the wizard showing an error after cancelling the deconvolution.
  • (E/P) Fuser:
    • Fix the application of the scale parameters (stretching/compression) to the images.
  • (E/P) Batch Feeder:
    • Fix Batch Feeder initializing very slowly on Windows when a directory containing a large number of tiff files is being watched.
  • (E/P) Image Stitcher:
    • Fix for tiles missing both proper meta data and name patterns indicating the offsets.

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.