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.

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What's new in Huygens 24.10 (To Be Released)

Huygens Professional, Essential, Localizer & Core

(E/P) Crosstalk & Autofluorescence Corrector:
- The Crosstalk Corrector has gotten a major revision, and is now named the Crosstalk & Autofluorescence Corrector.
  - An autofluorescence reference channel can now be provided to the tool, to estimate autofluorescence in and remove it from the other channels.
  - User interface:
    - Changed the user interface to a wizard structure, that guides you through the correction step by step.
    - It is now possible to compare MIPs of the original and the corrected image.
    - Expanded visualization options for the MIPs and histograms.
  - Crosstalk estimation: added a new estimation algorithm with the following advantages:
    - Improved performance on images with 3 or more channels compared to the old method.
    - Faster processing on large images.
  - Crosstalk correction: improvements were made to the correction step. This might affect reproducibility in some cases.
    - The datatype will now be scaled up when intensities exceed the original datatype's dynamic range after crosstalk correction.
    - Improved intensity preservation for data saved in unsigned datatypes.
    - Improved numerical stability. This mainly affects images with 5 or more channels.
  - Other changes:
    - Improved the noise reduction of the histogram.
(E/P/C) Array Detector STED deconvolution option:
- Added Array Detector STED Microscope type and theoretical multi-detector STED PSF model.
- Added an extra reduce option 'Core Best 3' automatically chosen:
  - For data with high lateral (2D) STED laser power.
  - When the outer detectors do not contain much biological signal compared to background.
(E/P/C) Deconvolution algorithms:
- Hybrid AI deconvolution:
  - Filament aware deconvolution is now available in Deconvolution Express (under Profile) and in the Deconvolution Wizard (under "Strategy for initial values").
- (CTM) Improve regularization for 3D widefield and brightfield images.
(E/P) Huygens Quality Control Tool:
- Added "Fast mode" which speeds up quality control calculations, especially for large images.
- The quality control options previously hidden behind the "Experimental options" are now normally available.
- Improved overall quality control results accuracy.
- Improved GUI.
(E/P/L) Huygens Workflow Processor:
- (E/P/L) Changed how the "Image selection" tasks work to add more features and make it easier to understand.
  - The "Select image series or container" task has been reworked to the "Extra file open settings" task. No longer mutually exclusive with "Select image(s)" but used to set extra options.
  - It is now possible to manually select subimages of multiple similar files or manually interpret multiple similar file series in one workflow designer window.
- (E/P) Hot and cold pixel task: It is now possible to add both a hot and cold pixel correction mask in a single task.
- (E/P) Stabilize Task: Add Array Detector Confocal Microscope type as supported microscope type for z-stabilization.
(E/P/C) Huygens Stitcher (Wizard and Workflow Processor task):
- Improve estimation accuracy for memory-mapping the result.
- Introduce a new "low-memory" option for the optimization in X, Y, Z that drastically reduces the memory requirements for 3D optimization on large images having large overlap percentage.
- Reduce the amount of recomputation for each tile during stitching, which is beneficial for very high numbers of tiles.
- Introduce a second method for estimating the vignetting parameters in the automatic vignetting correction.

Minor Changes

(E/P/L) LUT Editor:
- Update to the GUI:
  - Clearer distinction between contrast and color settings.
  - Edit the contrast and LUT settings of all channels at the same time.
  - More easily construct LUT from different gradients.
- LUT table exports can now better be read by ImageJ.
(E/P/L) Huygens Object Analyzer :
- Segmentation groups can be turned on and off more easily.
- Move the location if the time slider to below the rendering so it is always visible.
- Add buttons for saving the intensities and label image directly to disk.
- Executing a workflow that imports a segmentation multiple times no longer loads the segmentation each time.
- The default save format for the table is now .csv (was .txt).
- When both a MIP and a surface are active, the overlapping regions now respond better to the MIP threshold.
- Increase the maximum allowed sigma for the Gauss filter for undersampled images.
- (MacOS) The table right-click menu can now also be opened via Ctrl-click.
(E/P) Huygens Colocalization Analyzer:
- Removed Colocalization Analyzer Advanced as it led to confusion, and Compact has identical functionality.
- Renamed channels in user interface from Red/Green to A/B to avoid confusion with fluorophore emission colors.
- The default save format for the colocalization coefficients is now .csv (was .txt).
(E/P) Huygens Batch Feeder:
- Improve the handling of TIFF series. Based on the first TIFF files being loaded from the output folder, it is now possible for counters/numerals in the file name to select whether they indicate slices, channels, frame or detectors of the same image, or simply independent images.
- Added a refresh button, allowing to directly create tasks for newly added files in the watch folder.
- The Batch Feeder now waits with adding a tiff series task if an element of the series has been modified recently. This helps preventing starting the task before the image/file series is complete.
(All) File Formats:
- File Readers:
  - OBF: Added support for Array Detector STED microscope type and reading of processed TIMEBOW images, DYMIN/RESCUE probe images, and other supplementary images.
  - VSI: Added support for reading Olympus Slide Scanner (VS120) VSI files with JPEG2000 compression.
  - OME-TIFF: Added support for reading ome-tiff files with JPEG2000 compression.
  - CZI: Added caching of the metadata, speeding up reading many tiles from the same CZI file in the Stitcher.
- File Writers:
  - TIFF: Improved guidance for saving images as TIFF. Illustrate what happens to the intensity range of an image when saving as 8 or 16 bit TIFF and how the contrast stretch, linked scaling or clipping intensity modes influences this.
(E/P/L) File series tool:
- Added "Separate image" option for the pattern, this option opens the files as separate images without considering it tiles for stitching.
- Changed GUI to give more information on what images the currently set pattern interpretation results in.
(L) Huygens Localization Viewer:
- Enabled filtering on FWHM, FWHM-X and/or FWHM-Y column if present in the table.
(L) Huygens Cluster Analyzer:
- Add a mouse mode that allows to discard clusters from the analysis.
- The default save format for the table is now .csv (was .txt).
(E/P/L) Convert window:
- Improve the UI of the convert, mirror and rotate options, available from the main menu under Tools. Added illustrations explaining the available options.
(E/P/L) Main Window:
- When closing Huygens, notify about images that contain unsaved changes that are lost when closing the software. Add the option to save these images before closing.
- (L) When reading in a csv/txt table using File-> Import -> Import table, columns not fitting in one of the typed columns can be read into a Custom column. In the Localization Viewer it is possible to filter based on the custom columns.

Bugfixes

(E/P/L) Huygens Object Analyzer :
- Fix filtering objects on the x/y/z component of a distance not working.
- Fix analysis failing when the ROI has a very large number of disconnected components.
(L) Huygens Cluster Analyzer:
- Fixed filtering clusters on the x/y/z component of a distance not working.
(E/P/L) Export Rendering:
- Fix exporting renderings on Windows to allow non-ascii charachters in directory names.
(E/P) Huygens Movie Maker:
- Fix Surface Renderer preview not showing the correct coloring in some cases.
- Fix Surface Renderer movies with watershed segmentation enabled to flicker in rare cases.
(All) Miscellaneous:
- Fixed a bug where automatic cropping would not handle time series as intended.

What's new in Huygens 24.04

Huygens Professional, Essential, Localizer & Core

(E/P) Huygens Quality Control option:
- New option that can be added to your license to automatically investigate the quality of an image.
- This option can check the microscopic parameters, nyquist rates, SNR estimation, clipping, crosstalk, bleaching.
  - Additionally, "experimental options" are available for checking hot/cold pixels, detector alignment, chromatic aberration, stabilization and PSF shape in an image.
- Explanations about the issues are given, which helps with identifying and confirming the found issues manually.
- From the Quality Control option it is easy to correct the issues with restoration options already present included in your license.
(E/P/L) Huygens Object Analyzer:
- The UI of the Object Analyzer has been redesigned.
  - Most options are now collected in the left column of the Object Analyzer, distributed over extendable panels.
  - Many more icons have been added to make it easier to navigate the rendering and analysis options.
  - Added a bar with favorites, where you can pin buttons that you often use.
  - Added additional interactive tutorials for multi-channel data, time series and using the ROI.
  - Added color hints to make it easier to see which channel corresponds to which segmentation group.
  - Improved the filter window to make it easier to see which objects will be discarded.
  - Added presets to the filter window.
  - Added a right-click menu to the rendering.
- Double clicking on a statistics table row now centers the rendering on the corresponding object.
- Added a new mouse mode called "Select a cluster of objects" for selecting all objects belonging to a cluster.
- There are now two Object Analyzer license options available to the OA, the Object Analyzer Compact option and the Object Analyzer Advanced option. The former is more economical, the latter offer more features.
(E/P) Huygens Track Analyzer:
- Visualize the MIP projection over time.
- Options to more easily detect and fix possible flaws in the tracks:
  - Find tracks that might need to be connected.
  - Find tracks that might need to be split.
  - Find large objects that were incorrectly detected as two touching objects.
- It is now possible to add missed objects to tracks.
(E/P) Huygens Surface Renderer:
- The UI of the Surface Renderer has been redesigned.
  - Most options are now collected in the right column of the Surface Renderer, distributed over extendable panels.
  - Many more icons have been added to make it easier to navigate the rendering options.
- Added options for adding and customizing grid rulers.
(E/P) Huygens Batch Feeder:
- New options have been added to the Batch Feeder preferences to customize its behavior:
  - The depth of subfolders of the input to recursively search for images can now be changed.
  - It is now possible to preserve the input folder structure for the output folder.
  - It is now possible to automatically run the processing of the Batch Feeder upon startup of the software.
(P/L) Huygens Python Scripting:
- Python Scripting is now also available on MacOS
- NumPy is now included in the Huygens Python interpreter.
(L) Huygens Cluster Analyzer:
- Double clicking on a statistics table row now centers the rendering on the corresponding cluster.
- Improve the filter window: it is now possible to use a filter to keep clusters or discard them and to select a cluster group to apply the filter to.
- Added the localization density of the cluster convex hull, the h.Density parameter, to the Shrink wrap (convex hull) geometry preset.

Minor Changes

(E/P/L) Huygens Workflow Processor:
- Added option to add files in folders recursively.
- Added option to the saving options task for saving the results in the same folder as the original image.
- (L) Added the Analysis task to the Workflow Designer.
(E/P/C) Huygens Stitcher:
- Improved handling of low values with integer-typed tiles and integer-typed result.
(E/P) Deconvolution Express:
- Bleaching correction for time series of all microscope types is now enabled.
(E/P) Huygens MIP Renderer:
- Added options for adding and customizing grid rulers.
- Added some colors from the Matplotlib library.
(E/P/L) Huygens Object Analyzer:
- Clicking on a statistics table row corresponding to a cluster now adds all elements of that cluster to the selection.
- When enabling watershed segmentation, "Use sparse seed" is now enabled as default.
(E/P) (Twin) Slicer:
- Option to create an image of the current slice or MIP/Sum projection.
- Draw circles to measure radii of objects.
- Added some colors from the Matplotlib library.
(E/P/L) Rendering in the Object Analyzer, Surface Render, Cluster Analyzer, Colocalization tools:
- Improved visualization of Surfaces in combination with a MIP in very bright areas.
(All) File Formats:
- File Readers:
  - QPTiff: Added support for reading QPTiff's.
  - CZI: Added support for reading .czi files with new Zstandard (zstd) compression.
- File Writers:
  - OME TIFF: Added support for saving images as pyramid OME-TIFF.
(L) Workflow Processor:
- Made the localization 3D calibration parameters editable.
(E/P/L) Bug Reporter:
- Made it possible to send information about software issues directly to us when they occur.
- Made it possible to report an issue via Help->Report issue.
(E/P/L) Preferences Window:
- Added a new preference for a directory/folder to hold temporary data.

Bugfixes

(E/P) Deconvolution Express:
- Fix a resource leak in deconvolution of time series in cases with spherical aberration where the sub-brick (VarPSF) feature is used.
(All) File Readers:
- OBF: Fixed where multi-channel unprocessed MATRIX STED data would be read with wrong dimension orders.
(E/P/L) Huygens Object Analyzer:
- Fixed an issue where the "Fill enclosed cavities" option would fail when the number of cavities is very large.

What's new in Huygens 23.10

Huygens Professional, Essential, Localizer & Core

(E/P/L) Huygens Object Analyzer:
- (E/P) Track and Analyze objects over time (requires Object Tracking license).
  - It is now possible to link the segmentation of multiple individual frames to each other, allowing measuring how an object changes over time.
  - The linking will also produce tracks, which can also be used in the Track Analyzer.
- Importing label images for segmentation:
  - Import label images created by various other segmentation software packages (such as for example Cellpose, StarDist).
  - Imported 2D segmentations can also be merged slice-by-slice into a 3D segmentation.
- Add convex hull (shrink wrap around the object) based analysis:
  - Added options to use the convex hull of a selection of objects/anchors as ROI.
  - Added a new analysis preset for analyzing the geometry of an object's convex hull.
  - Added a new analysis preset for analyzing the distance between objects, based on their convex hulls.
- Measure surface-to-surface distances between objects and anchors/the ROI.:
  - Added parameters to measure surface-to-surface distances besides surface-to-Center of Mass
- Extended Watershed segmentation
  - Added additional "Use sparse seed" option for the watershed segmentation that can be used when splitting objects is hard to do with the other options.
- General performance improvements for the analysis.
- (E/P) Analysis Workflow Designer:
  - Added Cluster Analysis task to the Analysis workflows.
  - Added task for saving the rendered scene to a JPEG or RGB-TIFF image.
(E/P) Huygens Workflow Processor:
- Added Batch Colocalization Analysis.
  - Analyze multiple multi-channel time series images in one go.
  - All channel combinations from the selected channels will be analyzed.
  - Optionally perform background estimation (gaussian minimum, costes method, optimized search) or manually set thresholds in % of the total intensity.
  - The colocalization coefficients table gets exported to a csv file, and a colocalization map can optionally be saved for each channel combination.
  - Note: Region of Interest not yet possible.
- Added a "convert data type" task for the purpose of minimizing the size of the result image on disk.
  - Before saving, convert the result image to: 32bit float, 16bit (unsigned) integer, or 8bit unsigned byte (might require scaling of intensities to fit).
  - Or choose "Smallest without scaling", which automatically chooses the smallest size where the data fits without scaling.
- Added flexibility to select which results to save in the "save" task.
  - Option to not save the result image and/or used template.
  - Save additional results: image statistics, Maximum Intensity Projections (along X, Y or Z), and a Thumbnail image of the result.
(All) File Formats:
- Added a new file format "Memory Mapped File" with extension (.mmf) as alternative to SWAP
  - Loading Memory Mapped images bypasses the use of system RAM. All image processing with the opened image, will be done directly with the file on disk.
  - This can be used to process images that do not fit in RAM memory. The stitcher uses this format by default when the result image would otherwise not fit.
- Added support for exporting and reading of PNG images in Huygens.
- (E/P) Improved support for workflows with Abberior MATRIX STED images.
  - After opening file, the image is split into the raw 23-detector image, and a preview image of the summed central 7 detectors.
  - Improved support for opening these 23-detector images in the Array Detector Quality Control Tool.
(E/P/L) Huygens Slicer/Twin Slicer
- New contrast control options:
  - An 'auto' button which cycles through settings of increasing contrast.
  - A slider to edit the contrast range of a specific channel or all channels together.
  - A help button which explains the current contrast settings.
(E/P) Huygens Sitcher:
- Memory improvement: Reduced usage of 32-bit float images where possible.
  - Non-deconvolved images can be completely stitched in 16-bit integer datatype, saving memory.
- Use of the new memory-mapped file (.mmf) file format for temporary and result images when they would not fit in RAM (system) memory.
(E/P/L) Plot Window:
- Plots can now be saved as PNG or JPEG images.
(E/P/L) Huygens Object Tracker:
- The Tracking algorithm has been improved. This might affect reproducibility of existing tracking templates.
(L) Cluster Analyzer:
- Added a new preset to analyze the geometry of the convex hull (shrink wrap) of the clusters.
(E/P/L) 3D renderers:
- Added JPEG as export option of current view in MIP and SFP renderer.
(L) Cropper:
- Added option to crop Localization Tables.
(E/P/L) 2D histogram:
- This window has been updated. It now has various settings and it is resizable.

Minor Changes

(All) GPU acceleration:
- Dropped support for graphics cards with a compute capability lower than 5.0 (Cards older than ~2013). See https://svi.nl/gpucards#Huygens_23.10 for a list of affected cards.
- Dropped support for CUDA Toolkit versions lower than 11. In case you have an older CUDA Toolkit version installed, you will need to update it to a newer version to enable GPU acceleration in Huygens. See https://svi.nl/GpuChecklist for instructions.
(All) Huygens Everywhere:
- Rename the term "Group" to "License" to prevent confusion when having to choose between multiple license options.
(E/P) Huygens Fuser:
- Update the visualization in the side view when rotating the individual images.
(E/P/L) Huygens Object Analyzer:
- Have the conditions rows in the table display more information.
- Added option to import the ROI from the main window.
- Add a warning when trying to load an image with default sampling sizes in the Object Analyzer.
- Useful keyboard shortcuts, like Ctrl-z for undo, now always work when the Object Analyzer is active. Keyboard shortcuts for anchors hav been removed.
- Improve user interface for the frame slider and the segmentation settings.
- Improve tutorial text.
- Improve explanation for the Analyze clusters option.
- When there is only one ROI component, only print the main ROI row.
(L) Cluster Analyzer:
- When selecting a parameter to color on, the coloring is always kept up-to-date, i.e. recompute when the clusters change. Effectively auto-color option is now always on.
- Added customization of the scale bar.
(E/P/L) Microscopic Parameters Window:
- Improve multi photon parameters (photon count) option in the UI. Added a checkbox to indicate that data is acquired with multi-photon excitation.
  When the option is checked, the amount of excitation photons can be entered.
(E/P/L) Huygens Visualization Tools:
- Added more customization to the scale bar, including text size.
(E/P/L) Contrast/LUT editor
- Improve behavior of dragging control points, especially the end points.

Bugfixes

(All) Huygens Bleaching Corrector:
- Fix a rarely occurring bug which only happens for bleaching correction of confocal time series that do not exhibit the typical exponential intensity decay.
  This bug caused non-deterministic selection of one of 2 potential correction strategies.
  - Strategy 1: Correct all frames to match the summed intensity of the primary time frame
  - Strategy 2: Correct all frames to match the averaged intensities of all time frames.
(All) Microscopic Parameter Window:
- Fix a bug where manually edited parameters would not count towards accepted or verified status.
(All) File readers:
- Ome-Tiff reader:
  - Fix not being able to read ome-tiff files with a custom xml tag starting with Image in the ome-xml meta data, e.g. <ImageVersion .
(E/P/L) Huygens Object Analyzer:
- Fix File -> Export Rendering resetting the parameter coloring back to Label.
- Fix the Object Analyzer being counted too often in the Usage Report.
(L) Cluster Analyzer:
- Fix the iso-surface threshold not being correctly taken into account for iso-surface computations. This affects the IsoVol, Surface and RoughSph (VoxArea and RoughRound for 2D data) parameters in the Small clusters geometry preset.
- Fix visualization bug where exporting the rendering would reset the parameter coloring back to type 'Label'.
(E/P) Workflow Processor:
- Fix the "Duplicate" button not duplicating the analysis task.

What's new in Huygens 23.04

Huygens Professional, Essential, Localizer & Core

(All) Change in scripting with images/tables:
- Creating images or tables returns a handle instead of their name.
  - Handles are to be used for Tcl and Python scripting.
  - Previously, the image name served this purpose and images could therefore not be renamed.
- Rename images or tables without creating copies
  - Right-click the thumbnail and select "Rename Image/Table" or press F2 as a shortcut.
  - Use Tcl scripting with the rename command 'oldName rename newName'
(P/L) Python Scripting:
- Updated Python from version 3.7.8 to version 3.11.1
- Updated the Python image class to be compatible with image handles and image names.
(E/P) Deconvolution Express:
- Improved automatic SNR and Acuity estimation. The suggested Acuity can no longer be out of the normal range.
(E/P/C) Deconvolution algorithms:
- (CMLE/GMLE) Added a correction to the regularization for images with only one or two z slices.
- (CMLE) Improved the correction to the regularization for under and oversampled images. This change is almost disabled when acuity is disabled, for better backwards compatibility.
- Note: Deconvolution templates for shallow and/or very under or oversampled images might need adjustment.
(E/P) Workflow Processor:
- Added an "Analyze Objects" task for doing object analysis in batch (see below).
- Added "Automatic" deconvolution algorithm, which does deconvolution with automatically found settings like in the Decon Express.
- Added the option to do Crosstalk Correction by using a Crosstalk Correction Template.
(E/P/C) Batch Object Analysis
- It is now possible to do Object Analysis in batch by using a new task in the Workflow Processor.
- (E/P) The Workflow Designer in the Object Analyzer has been improved and modified to support batch processing.
  - The "Time frame and detector" task has been reworked to a "Time series" task. It is now possible to apply parts of a workflow to each time frame in an image. This replaces some old task specific options like "Analyze time series". Support for analyzing raw array detector images has been deprecated.
  - The "Set visualization task" has been deprecated.
  - In the "Basic ROI operations" and "Set anchor" tasks it is now possible to set the segmentation group for some options.
  - The "Advanced ROI operations" task has been expanded with more options.
  - A new "ROI intensity removal" task has been added which can be used to remove intensity from an image by using the ROI.
(E/P/L) The Object Analyzer
- Added a tutorial.
- (E/P) Reported parameters:
  - It is now possible to save and load custom selections of parameters using templates.
- Added the "HighContrast" parameters to the list of coloring parameters in the visualization tab. This parameter can be used to color objects in such a way nearby objects have contrasting colors.
- Added mouse modes for drawing selections in regular shapes.
- Analysis of 2D XY slices will no longer report parameters that are irrelevant or misleading for 2 dimensional images.
- Added/improved GPU support for merging and removing objects, selecting objects with the lasso tool, and for various analysis operations.
- Improve selection of objects. It is now possible to select multiple objects by using Ctrl + Left mouse button when in the analyze mouse mode. Selected objects will also be highlighted more clearly.
(E/P) Crosstalk Corrector:
- Added support to crosstalk corrector for unprocessed Array Detector images
- Added Crosstalk Correction Templates.
- Updated the Mip preview.
(All) File readers:
- HDF5 reader:
  - Read Luxendo metadata.
  - Added support for HDF5 images split over multiple files.
(C) Huygens command line interface (CLI):
- Start Huygens Core from a command line with paths to a workflow template and an image to apply that workflow template to that image.
  - With this it becomes easy to integrate Huygens deconvolution and processing in your custom workflows.
  - This makes it easy to implement Huygens with a job scheduler (e.g. Slurm).

Minor Changes

(E/P) Improved raw Array Detector image support:
- Added detector cropping option to the Cropper.
- Gallery tool can visualize slices across the detector images.
(E/P) SFP renderer:
- Use full resolution while rotating or zooming when this is fast enough.
(E/P/L) All renderers:
- Customizable scale bar.
(E/P/L) Slicer/Twin Slicer/MIP renderers
- Overlay hue bar that shows the look-up table of the image.
(E/P) PSF Distiller:
- Made the STED Parameter estimation optional. You can now directly export your distilled STED PSF as is.
- Lowered the allowed diameter for STED beads from a minimum of 25nm to 20nm to account for STED GATTA-Beads of 23nm.
- Improved suggested SNR value and allowed different SNR values for different channels when distilling multiple channels from one image.
(All) File readers:
- Abberior Msr/Obf:
  - Improved reading speed of chunked obf files containing large tile series and/or time series.
  - Fixed reading of the angle for rotated tile acquisitions in both Facility Line and STEDYCON files.
- Tiff reader:
  - Added support for tiled tiffs with 8/16 bit (unsigned) integer and 32 bit (unsigned) integer/float datatypes.
  - Partial support added for 32 bit integer tiffs. These will be read in and converted to (32 bit) float images.
- Ome-Tiff reader:
  - Improved reading in the data of a single file from a file series for special cases, for example files written by VisiView.
  - Improved attaching the channel meta data when loading a subset of the channels of the full image.
(All) File writers:
- Ome-Tiff writer:
  - Save all Huygens Microscopic parameters not fitting in the OME schema to a custom SVI StructuredAnnotation.
  - All Huygens Microscopic parameters are now saved when using the OME-TIFF format, including STED, SPIM and Array Detector parameters and the parameter reliability states.
(E/P/L) Export of rendering:
- Added the option to export to the Surface Renderer and Object Analyzer.
- Added the option to export without border at original size in the Slicers.
(L) Cluster Analyzer:
- Analysis of 2D tables will no longer report parameters that are irrelevant or misleading for 2 dimensional data and now contains relevant roundness measures for 2D data.
- New coloring options: it is now possible to color the clusters based on some of their properties. For instance clusters with the same parent can be given the same color.
- Add the "HighContrast" parameters to the list of coloring parameters in the visualization tab. This parameter can be used to color objects in such a way nearby clusters have contrasting colors.
(E/P/L) Preferences:
- (P/L) Add setting for the prefered scripting shell (Python or Tcl).
(E/P/L) License Window:
- Improve description when adding a license that does not work for the open product.

Bugfixes

(E/P) Deconvolution Express:
- Fixed a bug when not supersampling all but at least one Array Detector channel.
(E/P/L) Workflow Processor:
- Fixed small bugs that could happen when opening series files.
- (E/P) Fixed a bug when not supersampling all but at least one Array Detector channel.
(E/P/L) Twin Slicer:
- Fixed an issue where the right viewer of the Twin Slicer would not use the correct z-slice when the viewed images have different z-sampling.
(E/P/L) The Object Analyzer
- Fixed a rare issue where the analysis would not continue correctly when pressing the stop button during analyze all.
- Fixed an issue where parameters depending on the principal axes were not computed correctly for objects with negative principal components.
(E/P/L) The Object Tracker
- Fixed an issue where the training could fail when two channels are very similar.
(All) File readers:
- Olympus VSI: fixed crash when reading a file with a large number of acquisition markers.
(L) Cluster Analyzer:
- Fixed an issue where parameters depending on the principal axes were not computed correctly for objects with negative principal components.

24.04.0p7

(16th of October 2024)

(E/P/L) Object Analyzer:
- Fix some parameters not being visible in the Workflow Designer;
- Fix an issue where some parameters would not get computed for the ROI rows while a coloring is active;
- (Windows) Fix an issue where when using an imported segmentation, the name of the label image was not shown correctly.
(E/P/L) Chromatic Aberration Corrector Wizard:
- Fix issue where wizard crashes when loading a template generated in the Chromatic Aberration Corrector Window.
(E/P) Track Analyzer:
- Improve binning in histogram plots showing track statistics.

24.04.0p6

(1st of October 2024)

(E/P/L) Object Analyzer:
- Add new parameters named r.ColocV and r.RelColocV for measuring the intersection with the ROI.
- Fix an issue when loading a template which uses more channels than possible for the loaded image.
- Fix a regression introduced in 24.04.0p4 that caused analyzing many objects to take more time than needed.
- The time frame index is now always reported in the table when analyzing time series.
(E/P/L) Workflow Processor:
- Fix an error when trying to load a template with an analysis task with a filter step.

24.04.0p5

(26th of August 2024)

(E/P) Workflow Processor:
- Fix for lingering .ome extension which was not properly removed when batch processing .ome.tif images.
(E/P) Huygens Stitcher:
- Add reading of stage offsets for single-image VSI files, so they can be loaded from the Stitching & Deconvolution Wizard.
- Fixed an issue that caused a loss of data after converting the stitched result image to smaller datatype in the final stage.
(All) File Formats:
- MSR: Fix metadata reading for .msr files written with an updated version of ImSpector.
(L) Main menu:
- Fix the Twin Slicer short-cut not being enabled when selecting two images, only for a single image.
- Fix the Histogram tab for a table failing to compute the histogram for columns with the same value for all localizations.

24.04.0p4

(25th of July 2024)

(E/P/L) Object Analyzer:
- Fix an issue causing the "keep object" filter option to not work in some cases.
- Fix an issue where exporting the rendering would not work when the Workflow Processor, Coloc Analyzer or Cluster Analyzer had been opened before.
- Fix an issue where analyzing a single object after analyzing clusters could cause errors.
(E/P) Surface Renderer:
- Fix an issue where exporting the rendering would not work when the Workflow Processor, Coloc Analyzer or Cluster Analyzer had been opened before.
(E/P) Workflow Processor:
- Fix an issue where stitching particular Tiff series could fail.
(L) Cluster Analyzer:
- Fix a regression introduced in 24.04.0p0 causing an exported statistics table containing a mistake for the "Applied filters". The reference value or parameters were incorrect (last entry of the line).
(All) File readers:
- VSI: Fix a possible crash when reading certain VSI images.
- VSI: Fix z and t sampling unjustly being reported as read from file in some cases.
- CZI: Improved file reading speed for very large CZI files
- CZI: Improved search for Metadata in CZI files where the main "ZISRAWMETADATA" segment could be deleted.
- ND2: Fix case where (SoRa) Spinning Disk images would not be read in correctly.

24.04.0p3

(2nd of July 2024)

(E/P/L) Surface Renderer and Object Analyzer:
- Use global colors by default when this is set in the main window.
(E/P) Movie Maker:
- Fix movies using the Surface Renderer failing to save in rare cases.
- Fix flickering when creating a movie while using the "High Contrast" option in the Surface Renderer
(E/P) Bleaching Corrector:
- Fix bleaching templates created in the 24.04 not being loaded in correctly in the Bleaching Corrector.
(All) File Writers:
- OME-TIFF:
  - Fix saving an image as pyramid OME-TIFF not working correctly for unsigned 16 bit integer data.

24.04.0p2

(4th of June 2024)

(L) Cluster Analyzer:
- Add the "Correlation between channels" preset to analyze the distance of a cluster to its nearest neighbors in the other cluster group.
- Expanded the parameters on which the color assignment of the cluster can be based on with:
  - The distance to the nearest neighbor in the same/other cluster group;
  - The percentage of voxels of the cluster intersecting with a clusters of the other cluster group.

Bugfixes

(P/E) Stitching & Deconvolution Wizard:
- Fix regression introduced in 24.04.0p0a where the tile pattern as read from metadata would be overwritten, even without editing the 'Acquisition pattern' or 'Acquisition overlap'.
(L) Cluster Analyzer:
- Fix a regression introduced in 24.04.0p1. The DBSCAN clustering algorithm only worked once each channel (expect the one being currently clustered), has been clustered before, using FOCAL. Only affects multi-channel tables/data.

24.04.0p1

(29th of May 2024)

(E/P) Image Quality Control Tool:
- Now keeps track of the correction tools used and reports their usage in subsequent Quality Control reports.
- Fixed bug with Stabilization Quality Control where some time serie images were always marked as needing a correction.
(All) GPU processing:
- Improved the performance of single channel histogram computation on the GPU.
(All) File Formats:
- File Readers:
  - OME-TIFF: Fix an issue where Array Detector images saved from Huygens as "One file per detector" could not be read in again correctly.
  - OME-TIFF: Fix an issue where the Array Detector spacing parameter was not read back in correctly for images saved from Huygens.
  - TIFF: Read 16bit signed integer Tiff's into a (16 bit) signed integer Huygens image instead of an unsigned image.
- File Writers:
  - OME-TIFF: Fix a failure when saving images of less then 256 pixels in X or Y as pyramid OME-TIFF.
(All) Huygens Everywhere Login Window
- Made it possible to show/hide the password entry before logging in.
(L) Table cropper:
- Fix cropping a table which is already cropped/which itself is output of the table cropper not working.
(E/P) Stitcher:
- Improved behavior of overlap and columns entry boxes.
(E/P) Deconvolution Wizard:
- Improved behavior of acuity entry box.
(E/P/L) Object Analyzer:
- Fixed an issue where it could be impossible to select columns are cells in the table under some circumstances.
- Fixed the "Add anchors to ROI" option showing an error in some cases.
- Improved behavior of sorting the table after analyzing a time series.
(E/P) Surface Renderer:
- Fixed the rendering being stuck on the first frame for time series.
(L) Cluster Analyzer:
- Fix analyzing a channel with DBSCAN setting the cluster of all localizations to 0 in the table for all other channels. Only multi-channel tables are affected. This prevents:
  - Move localizations to main window leading to a table where only the last analyzed channel with DBSCAN has actual clusters not 0.
  - Updating the rendering of a channel not lastly clustered with DBSCAN, by changing the Render mode or FWHM lets all clusters of that channel/Cluster group disappearing from the rendering and analysis.
- Fix a rare bug that DBSCAN that could change analysis results for touching clusters. DBSCAN with "Ignore border points" is not affected. The Cluster column in the exported localization table is also not affected.

23.10.0p7

(11th of April 2024)

(All) File Formats:
- CZI: Fixed a regression introduced in 23.04 in the CZI reader for Linux when reading CZI files with jpegxr compression.
- CZI: Fixed an issue where reading Raw Airyscan data from very long file names would not succesfully open in Huygens.
- CZI: Add improved lightsheet thickness parsing for new czi files from Zeiss Lightsheet Z1 microscopes.
- OBF: Fixed where multi-channel unprocessed MATRIX STED data would be read with wrong dimension orders.
(All) Window management:
- Fix newly opened tools sometimes being placed on wrong monitor in multi-monitor setups.
(E/P) Workflow Designer:
- Improve deconvolution workflow for regular Tiff series written by Andor software.
(E/P) Twin MIP
- Fix bug where in specific situations the Twin MIP wouldn't start on single channel images.
(E/P) Deconvolution Express:
- Fix a resource leak in deconvolution of time series in cases with spherical aberration where the sub-brick (VarPSF) feature is used.

23.10.0p6

(27th of February 2024)

(All) File Formats:
- CZI: Fixed a regression introduced in 23.04 in the CZI reader for Linux when reading CZI files with jpegxr compression.
- TIFF:
  - When writing a tiff that requires scaling, add an option to open the help page on the website.
  - Fix parsing the geometry for plain Tiff's with a resolution unit of inch or centimeter.
- OME-TIFF: patch reading of files with inconsitent namespace usage in the xml w.r.t. OME attribute and its child attributes.
(E/P/L) Object Analyzer:
- Fix a rare bug that could lead to incorrect surface to surface and convex hull distances, specifically the parameters: a.Hull, a.sSurf, r.sSurf.
- Fix an issue where the segmentation could reset unexpectedly.
(E/P) Deconvolution Templates:
- Fixed bug where the Array Detector Reduction Mode was not properly added to GMLE deconvolution task templates.
(E/P/L) Cropper :
- Prevent an image with a time dimension of 0 from resulting in a cropped image with a time dimension of 1.

23.10.0p5

(25th of January 2024)

(E/P) Twin MIP:
- Fixed that the movie was saved twice when saving a movie from the Twin MIP while linking as "color and channels" or "everything".
(E/P/L) Slicer:
- Fixed a bug where "Clone this slicer" did not synchronize the time frame, this also caused bugged behavior when creating a plot in a different time frame than 0.
(E/P/L) Workflow Processor:
- Fixed a bug for container images with sub-sub-images, where results could overwrite each other in some situations.
(P) Operations Window:
- Fix for the mirror operation to mirror the entire raw Array Detector dataset instead of only the first detector when mirroring in Z and T.
(E/P) Object Analyzer:
- Fix an issue causing changes to the current time frame to not be logged to the history is some cases.
- Fix the ROI cropping option.
(E/P) Movie Maker:
- Fix an issue where the rendering could have sudden moves when the zoom is high.

23.10.0p4

(8th of December 2023)

(All) General:
- Linux: add support for Ubuntu 23.10.
(All) File Formats:
- OME-XML: fix a regression breaking the OME-XML writer since the 23.04 release.
(E/P) Movie Maker:
- Fix a regression introduced in 23.04 release, causing the movie maker not to work with the MIP renderer when adding more than 4 key frames.
(E/P) Stitcher:
- Fix for loading manual vignetting correction images defined in templates.
- Added incompatibility warning for the "Automatic" deconvolution algorithm, which cannot be used when stitching.
(E/P) Deconvolution Express:
- Changed Acuity sliders responsiveness, new deconvolution previews will now generate after releasing the mouse button.
(L) PSF Distiller:
- Fix a regression introduced in 23.04 release, causing an error when distilling a multi-channel PSF from astigmatic 3D SMLM data.
(E/P/L) MIP/Twin MIP renderer:
- Changed contrast options to match the new contrast options in the Slicer and Twin Slicer.
- Improved syncing of color and contrast settings in the Twin MIP renderer.

23.10.0p3

(30th of November 2023)

(All) File Formats:
- OBF: Add back the filename in front of the sub-images when loading new Facility Line OBF images which was removed since version 23.10.0p0.
- Tiff: improve reading pixeldata from 16-bit signed tiffs with intensity offsets as written by ImageJ containing negative values.
(E/P/L) Microscopic parameter editor
- Fixed a regression introduced in 23.10.0p0 causing the multi-photon option and photon count only being editable for the first channel.
(L) Localizer main window:
- Fixed the Tools-> Join Images main menu bar option not working if there also is a table in the thumbnail selection, regression introduced in 23.04.0p0.
(L) Cluster Analyzer:
- Fix the Cluster Analyzer freezing when first selecting another parameter to color on than ClusLabel or RandomClusLabel and then deselecting this cluster pipe, e.g. setting the channel to off.

23.10.0p2

(17th of November 2023)

(All) Deconvolution
- Fixed a memory safety error for very large images when finding the optimal bricking layout.
- Fixed an integer overflow in the PSF generation for very large images with spherical aberration.
(All) File readers
- Improved memory safety in the .msr and .obf file reader.
- Fixed metadata issue for .lif files introduced in 23.04.0p0.
(E/P) Object Tracker
- Fixed a regression introduced in 23.10.0p0 where the Tracker would always use the first frame to train on.
(E/P/L) Object Analyzer
- Fixed an issue where the "Fill enclosed cavities" option would sometimes not remove all cavities when the GPU was enabled.
- Fixed an issue where loading a template in the Workflow Designer with two automatically segmented channels would not set the channels correctly.
(E/P) Object Stabilizer
- Fixed an issue where stabilizing time series using the Tracker was sometimes disabled.

23.10.0p1

(9th of November 2023)

New features and minor changes

(E/P/L) Workflow Designer
- Improve processing speed when selecting multiple image files at once for the "Select Image(s)" task.
(C/P/L) Huygens Python
- Command line arguments can now be up to 4096 characters long, up from 128.

Bugfixes

(All) File Readers
- OBF: Fix file reader when opening new DyMIN and Rescue STED images written with Abberior Lightbox version 2023.26 and newer.
(E/P) Deconvolution Wizard & PSF Distiller
- Fix crash during STED PSF parameter estimation when image name 'psf' is not available.
- Fix crash that occurred when deconvolving images with very large dimensions (larger than 10,000 x 10,000 pixels).
(E/P) Object Analyzer
- In the Workflow Designer, fixed the "Open in Workflow Processor" button not working correctly.
(C/P/L) Huygens Python
- Fix Windows not being able to import modules like scipy due to missing python libraries.
- Fix an issue where image.toNumpy and image.fromNumpy did not work even when numpy was imported.
- Fix an issue where image.toNumpy and image.fromNumpy would use a wrong dimension ordering.
(P) Operations Window:
- Fix a regression introduced in 23.04.0p0 causing the Multi-GPU versions of CMLE, QMLE and GMLE not to work.

23.04.0p7

(18th of October 2023)

(E/P/L) Thumbnails:
- Fixed thumbnail brightness inconsistencies when switching between 2D and 3D modes.
(E/P) Workflow Processor:
- Fixed the issue where loading custom darkframe and flatfield images in the Stitching task was not possible.
(C) SNR utilities for the HRM:
- Fixed regression introduced in 23.04.0p0 for the "Legacy" SNR estimation in the HRM that caused it to never work.
- Fixed bug for the "Auto" SNR estimation in the HRM where the shown previews were not correct when an intermediate step for SNR estimation failed.
(E/P) Movie maker:
- Fixed issue with downsampling that resulted in an error when using the Movie Maker with the Surface renderer.

23.04.0p6

(14th of September 2023)

(All) File readers:
- OME-TIFF: Fixed regression introduced in 22.10 causing for some files to read in only the first slice instead of the full z-stack, for example some ImSpector exported data.
- CZI:
  - Fixed an issue where images with invalid wavelength values could not be opened.
  - Fixed an issue where backprojected pinhole values where not estimated correctly when only a few channels have metadata for them.
  - When the microscope type cannot be determined from the metadata, use "confocal" as default.
(E/P/L) Object Analyzer:
- Fixed an error when hovering over an object after sorting the table.
(E/P/L) Hot & cold pixel remover in Workflow Processor:
- Fixed a bug where for images with a particular dimension setup a valid mask image would be rejected as having the wrong dimensions.
(E/P) Interactive Fuser:
- Fix regression introduced in 23.04.0p0 where image data could not be processed in the fusion steps.
  *Applies only to data where all rotational views are opened from a single container image file format like .CZI or .LIF files.
(E/P) Array Detector Quality Control Tool:
- Change default value of intensity coloring to scale with respect to the detector with maximum intensity instead of central detector.

23.04.0p5

(24th of August 2023)

(E/P) Array Detector Quality Control Tool:
- Add support for Airyscan 2 images;
- No longer show the "Shift" tab for preprocessed detector models for which shift computations are not possible.
(L) Cluster Analyzer:
- Fix the auto color option not working correctly when enabling this option with an out-dated clustering, i.e. changing cluster parameters without pressing Cluster & Render and then enabling the auto-color option in the Visualization tab.
(L) Localizer:
- Improve the localization of rare particles where the initial guess has a negative intensity after background subtraction. This might add localizations to the final result as such these rare particles are no longer directly discarded. The values of the other localizations are unaffected.
(E/P) Object Stabilizer:
- Use a more notable button for entering the wizard.
(E/P/L) User Interface:
- Improve the contrast of the highlighted text for some entry boxes.

23.04.0p4

(25th of July 2023)

New features and minor changes

(E/P/L) Object Analyzer (Basic):
- Add convex hull based analysis.
  - Added option to set the ROI to the convex hull of a selection of objects.
  - Added two new analysis presets: for analyzing the geometry of the convex hull of an object and for distance between objects based on their convex hulls.
  - On-the-fly visualization of the convex hull when hovering over a convex hull related parameter in the statistics table.
- (E/P) Improve settings in the segmentation task of the Analysis Workflow Designer
  - Separate the entries for the threshold, seed, and sigma when doing automatic estimation, instead of one setting that controls all.
- (E/P) Add option to load a different ROI for each input image in to the "Load ROI from file" option.
- Extend file formats used to read and write ROI's from just hdf5 to hdf5, ics, ome-tiff and tiff.
(All) Hot & Cold Pixel Corrector:
- Changed detected hot/cold pixel overlay to be drawn on the result on the right, for easier comparison with the original hot pixels on the original on the left.
- Overlay visualization option is now a checkbox that either shows or hides the Hot/Cold Pixel Mask on top of the result image.
(All) File readers:
- IMS: The Brightfield microscope type is now read from new Imaris files.
- MSR: Parse objective information for imspector .msr files.
(All) Rename tool:
- Improved scalability of rename window for larger image names.
(E/P) File series tool:
- Allow users to open tiles from a file series in the Huygens main window instead of forcing them directly to the Stitcher.
(C) Command line interface:
- Allow setting which GPU device to use for a template by using the -gpuDevice option on the command line.
(E/P) Colocalization Analyzer:
- Extend file formats used to read and write ROI's from just hdf5 to hdf5, ics, ome-tiff and tiff.

Bugfixes

(E/P) QMLE Deconvolution:
- Fix issue where early stop requests during QMLE deconvolution would not result in the end of the deconvolution run.
(All) File readers:
- OBF: Fix for Facility Line and Infinity Line .obf files only showing separate channels due to new version number schema in OME-XML metadata.
- TIFF: Fix a rare issue where only the first slice was loaded on Linux.
(E/P/L) Workflow Designer:
- Fixed a bug when using the fileseries tool with the ignore or "numerical" setting.
- Fixed a bug for stitching templates where the channels used for stitching would unintentionally reset.
- Fixed a bug where loading a template with the "Load ROI from file" option would give an error.
- Fixed a bug where loading a decon template with a single deconvolution task set all 32 channels to verified.
(E/P) Deconvolution Wizard:
- Fixed a crash when processing a multi-photon image with negative values.
(E/P) Stitching Wizard:
- Fixed a bug where templates were not accepted due to a non-existing mismatch in dimensions.
(E/P) Colocalization Analyzer:
- Fixed an issue where the Colocalization Analyzer Compact & Advanced tools could not start with RBNCC options enabled.
(L) Cluster Analyzer:
- Fix an issue where clustering the same channel with different settings in both pipes, could go wrong in a rare case.
  - When first clustering the channel in pipe A, then the clustering (the same) channel in pipe B and finally the visualization settings Render mode and/or FWHM of pipe A are changed, pipe A copied the clustering of pipe B in the rendering and analysis. Here clustering means pushing the Cluster & Render button.
(L) Localizer 2D/3D:
- Fix a rare crash during the localization on Linux.

23.04.0p3

(3rd of July 2023)

(All) Deconvolution:
- Fixed regression from 23.04.0p0 resulting in sub-optimal results for densly (over)sampled confocal images at larger iteration counts.
- Improved Signal to Noise Ratio estimation for non-descanned detector Multi-photon images.
(E/P) Deconvolution Wizard/Express:
- Added an extra check for NA and refractive indices to prevent potential crashes in the Deconvolution Wizard and Deconvolution Express.
(All) Workflow Processor:
- Print image names instead of image handles in the progress report of the workflow processor.
(All) File reader:
- All: Fixed regression from 23.04.0p0 resulting in "File does not exist" errors when trying to read files that contain consecutive spaces in the filename.
- LIF: Improved reading of the emission wavelength for widefield .lif images.
- MSR/OBF: Add imspector XML metadata parsing for Expert Line .msr files.
- TIFF: Add better support for reading pixeldata from 16-bit signed tiffs with intensity offsets as written by ImageJ.
(C) Command line interface:
- Fix issue where the default value for the -imgOpen CLI option caused a template to fail. (This affected HRM.)
(L) Object Analyzer Basic:
- Fixed Cluster Analysis not finding any clusters.
- Fixed some coloring parameters not working.
(All) GPU support
- Fixed regression from 23.04.0p0 where Cuda Toolkit version 11.6 could not be used with Huygens 23.04.
(P/E) Chromatic Aberration Correction Wizard:
- Fix for the error messages "Value for 'threshG' is below range: resetting to 0.000000" for integer-typed images with very low values.

23.04.0p2

(2nd of June 2023)

(C) Fix locale issues for HRM and HuCore users
- Prevent problems that could arise from the potential use of the comma (,) as decimal separators instead of period (.).
(All) File reader:
- MSR/OBF: Fix issue where images would only open up as separate channels. (Affected versions were 23.04.0p0 and 23.04.0p1)

23.04.0p1

(1st of June 2023)

(All) File reader:
- Olympus VSI: Prevented crash when trying to open an invalid VSI file.
- OME-TIFF: Fixed regression from 23.04.0p0 introducing a potential memory leak.
(E/P) Workflow Processor:
- Ensured the correct names are used when saving series images.
- Fixed getting a lot of warnings about Chromatic Shift Correction in some situations where it was not used.
- Fixed error when trying to execute an analysis template that shifts the ROI.
(P) Operations Window:
- Fixed issue where results of operations were not shown when using images a, b, c or psf as output.
(C) Command line interface:
- Prevented problems when using the -series option in HuCore intended as argument for a script.

Huygens Remote Manager 3.10

It is with great pleasure that we announce the immediate availability of HRM 3.10.0!

This is a release with various bugfixes that also adds support for Abberior MSR and OBF file formats.

For more detailed information and the included new features, we like to refer you to this website.

HRM 3.10.0 can be downloaded 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)

If you are interested in experiencing the HRM 3.10 userinterface, you can also have a look at http://hrm.svi.nl.

For older release information see: WhatsNewArchive.

Scientific Volume Imaging

Deconvolution - Visualization - Analysis

New features in Huygens Software

What's new in Huygens 24.10 (To Be Released)

Huygens Professional, Essential, Localizer & Core

What's new in Huygens 24.04

Huygens Professional, Essential, Localizer & Core

What's new in Huygens 23.10

Huygens Professional, Essential, Localizer & Core

What's new in Huygens 23.04

Huygens Professional, Essential, Localizer & Core

24.04.0p7

24.04.0p6

24.04.0p5

24.04.0p4

24.04.0p3

24.04.0p2

24.04.0p1

23.10.0p7

23.10.0p6

23.10.0p5

23.10.0p4

23.10.0p3

23.10.0p2

23.10.0p1

23.04.0p7

23.04.0p6

23.04.0p5

23.04.0p4

23.04.0p3

23.04.0p2

23.04.0p1

Huygens Remote Manager 3.10

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