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Archive for older Huygens releases


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, S = Huygens Scripting, C = Huygens Core, T = Huygens Titan. For information about newer releases see: WhatsNew.


17.04 Release


Highlights

Huygens Professional & Essential

  • SPIM:
  • GPU Deconvolution:
    • Full support for the variable PSF mode in CMLE and GMLE.
  • Batch Processor:
    • Multi GPU support.
    • Stabilization in Batch mode.
  • GUI:
    • Scalable user interface.
    • Day and night themes.
    • Support for 4K monitors
  • File readers:
    • Support for Andor TIFF.
    • Support for Metamorph ND.
  • New Bleaching Corrector

Minor changes

  • (All) CZI reader:
    • Support for JPEG-XR compression.
  • (All) ICS reader/writer:
    • Support for parameter states.
    • Support for SPIM parameters.
    • SVI now maintains the open source libics library for reading and writing of ICS data. Since Huygens uses libics the library will be released in sync with Huygens from now on.
  • (All) TIFF reader:
    • Support for 32-bit float files.
  • (All) LOF/XLIF readers:
    • Support for DSL data.
  • (All) OME-TIFF reader:
    • Metadata is loaded.
  • (All) GPU support:
    • Made switching to a different GPU device more robust
  • (E/P) Huygens - LAS X:
    • Faster communication and data transfers.
  • (E/P) Stitcher:
    • Improved support for custom stitching patterns.
    • More visualization controls.
    • A new MIP visualization mode.
    • Better performance and less memory consumption.
    • Disable background estimation and bleaching correction for the tile deconvolution.
  • (E/P) Batch Processor:
    • Improved GUI.
    • Support for loading LIF files with multiple levels of sub-images.
  • (E/P) Improved icons.
  • (P) Improved image convert window.
  • (E/P) Crosstalk corrector:
    • Reduce noise option
    • Correction is now energy conservative.
  • (E/P) Tab completion is available in the open file window on Linux.
  • (C) SFP renderer:
    • Threshold data by Otsu's method for rendering raw and deconvolved images.

Bug fixes

  • (All) CZI reader:
    • Fix 'Scale if necessary'.
  • (All) LIF reader:
    • Several fixes.
  • (All) ND2 reader:
    • Several fixes.
  • (All) Background estimation:
    • Fix background calculation on the CPU for floating-point images containing integer values.
  • (E/P) Drag & Drop:
    • Fix Windows and Linux distributions.
  • (E/P) Communication with Leica's LAS X software:
    • Fix floating licenses.
  • (E/P) Histograms:
    • Fix potential bug in the calculation of 5+ channel histograms.

17.04.1p2
(20th October 2017)
  • (All) Split channels:
    • Fix regression that caused the split command to ignore channel meta data.
17.04.1p1
(18th October 2017)
  • (All) Coverslip Editor:
    • Fix wrap around effect on deconvolution for negative coverslip positions.
  • (All) Split channels:
    • Fix potential error in the confidence levels of the extracted channels.
  • (E/P) HyVolution:
    • Fix deconvolution of STED 3X channels with very short PSFs previously failing at the Z stabilization step.
17.04.1p0
(2nd October 2017)
  • (All) HDF5 files:
    • Fix occasional hard error while loading images.
  • (All) ND2 files:
    • Fix occasional hard error while loading images.
  • (All) Metamorph ND files:
    • Fix loading old versions.
  • (All) GPU deconvolution:
    • Fix a problem in the fall-back from the GPU to the CPU in case the GPU encounters a problem due to e.g. lack of available memory.
  • (All) Windows:
    • Fix initialization of GPU device(s) when using CUDA 9.
  • (E/P) File Series Tool:
    • Fix occasional error when the files names have too many patterns.
  • (E/P) Fusion Wizard:
    • Fix deconvolution and microscopic parameters template buttons.
17.04.0p9
(15th August 2017)
  • (All) GPU processing
    • Use a sufficiently large string to report the names of all GPU cards.
  • (E/P) Decon Express:
    • More consistent SNR reports.
  • (E/P) Colocalization Analyzer:
    • Fix inaccuracies in computation of Pearson coefficient with a mask image.
  • (E/P) Cross-talk Corrector:
    • Fix potential low level error.
  • (E/P) Chromatic Aberration Corrector:
    • Fix interpretation of templates where there are missing values. This fix also affects the Batch Processor where the corresponding job could fail due to the missing value.
    • Editing the table is now slightly easier. Allow for empty cells.
  • (E/P) Batch Processor:
    • Add a new cascading menu to set the input conversion format for integer-typed input images to either int (the default) or float.
    • Fix interpretation of no stages in Metamorph .nd files.
  • (E/P) Stitcher:
    • Fix regression introduced in previous patch which rendered the quick launch button useless.
  • (P) Enable/Disable 'Split' entry in 'Tools' menu depending on context.
17.04.0p8
(18th July 2017)
  • (All) Compute Engine:
    • Fix unresponsive 'genpsfExpl' command.
    • Fix GPU initialization that would disable the GPU as a whole with more than 3 GPU devices present.
  • (All) ICS files:
    • Limit the number of channels to 32.
  • (All) HDF5 files:
    • Fix a crash and convert it into a regular read error when reading a certain HDF5 file (with invalid data).
    • Fix a crash on reading scaling data from a multi-channel HDF5 file.
  • (All) OME reader:
    • Report an error in case of an invalid number of channels or an invalid channel number.
  • (All) LIF reader:
    • Fix SPIM excitation mode.
  • (E/P) Stitcher:
    • Fix neglected channels in TIFF series.
    • Fix layout optimization of mosaics containing very noise as well as signal-rich tiles.
    • Fix occasional 1-pixel wide artifacts at the borders.
  • (E/P) SFP Renderer:
    • Fix table switch.
  • (E/P) Deconvolution Wizard and Deconvolution Express:
    • Fix occasional glitches in report area.
17.04.0p7
(30th June 2017)
  • (E/P) Twin Slicer:
    • Fix focus issue of the contrast window in Windows.
  • (E/P) Batch Processor:
    • Fix incorrect undersampled highlighting in microscopic templates.
    • Fix saving error of files containing unsupported path symbols (e.g. colon symbol) on Windows.
    • Fix missing update of the screen after loading a batch job list from file (new list was not shown in some cases).
  • (E) Fusion Wizard:
    • The tool is now available in Huygens Essential.
  • (All) Deconvolution:
    • Fix SNR multichannel report which failed to concatenate the single channel strings.
    • Fix small memory leak in the GPU version of GMLE.
    • More accurate background estimation of extremely low signal images.
  • (All) LIF files:
    • Read transmission channels as brightfield.
  • (All) HDF5 files:
    • Report when the file has been generated with a newer Huygens version.
  • (All) Metamorph ND files:
    • Fix case where there's only 1 position in a multi stage file.
17.04.0p6
(9th June 2017)
  • Fix occasionally incorrect background report.
  • Addition to preference window; the user can change what happens after a double clicking on a thumbnail in Huygens Professional: Open a slicer, twin slicer, MIP renderer or orthoslicer.
17.04.0p5
(1st June 2017)
  • Slightly smaller font for the Tcl shell.
  • Microscopic Parameter Editor: fix reported Nyquist rate for SPIM which did not take excitation mode into account.
17.04.0p4
(24th May 2017)
  • Fix error on closing the preferences window while the GUI was scaling.
  • Remove automatic DPI scaling which gives errors on OSX.
17.04.0p3
(19th May 2017)
  • Fix 'Experimental Presets' in Object Analyzer.

16.10 Release

Highlights

Huygens Professional & Essential
  • Automated, one button deconvolution via the new "Deconvolution Express" option:
    • A new method to do "unsupervised deconvolution" allows the user to get a quick, effortless deconvolution result, requiring no further user action.
    • Via right-clik on the image or via the main menu -> Deconvolution -> Deconvolution Express.
    • If needed, the user can fine-tune the method used for unsupervised deconvolution. Deconvolution Express offers a choice of fast, standard, conservative or aggressive methods.
    • Huygens can estimate several parameters such as the SNR based on image meta data and image structure.
  • Deconvolution:
    • GPU support for the most commonly used type of background estimation: the 'lowest' background mode.
    • Improved adaptation of brick layout to the available GPU memory
  • SPIM:
    • New sheet types now include Multi View 'MuVi', Bessel beam, two-photon Bessel beam.
    • Improved strip-like layout of bricks, adapted to the GPU memory if a GPU is available.
  • Object Stabilizer:
    • New and improved interface for the Object Stabilizer.
    • GPU support for cross correlation stabilization method.
  • Chromatic Aberration Corrector:
    • GPU support for the shift correction method.
  • GPU acceleration:
    • Support for CUDA toolkit 8.0.
  • New Huygens Server for communicating with Leica's LAS X software:
    • Possibility to exchange data between Huygens and LAS X.
    • Specify your LASX version in the Huygens preferences window.
    • Huygens can deconvolve imported images automatically by using the infrastructure of the new "Deconvolution Express".

Minor changes

  • (All) Background estimation:
    • Improved pre-filtering of the image when calculating the "WF" mode.
  • (All) GMLE deconvolution:
    • improved handling of very shallow or 2D images.
  • (All) Windows installer:
    • Warn the user if Huygens is running when there's a request for uninstalling or reinstalling the software.
  • (All) GUI:
    • Default thumbnails size is now chosen according to the monitor size.
    • The numerical keypad's "enter" key behaves in the same way as the main keyboard's "enter"/"return" key on Linux and Mac.
    • The "enter" key invokes the selected option instead of the default option in questions with multiple answers.
  • (All) CZI reader:
    • Add support for cases where the ZISRAWDIRECTORY segment is missing.
    • Fix case where the pinhole of one of the channels is missing.
    • Update internal magnification of LSM800.
  • (E/P) Colocalization Analyzer:
    • Extra column in the results tab to show the contribution of each object to the total coloc coefficient.
    • Background value can be set to 0.
    • Improved return value handling in Tcl coloc command.
  • (E/P) Stitcher:
    • Improve support for custom stitching patterns.
    • Allow 0% tile overlap.
  • (E/P) Communication with Leica's LAS X software:
    • Show 3 decimal digits at most in scaling factors.
    • Add XML headers to Huygens attachments.
  • (E/P) Object Analyzer:
    • Improved performance.
  • (E/P) Track Analyzer:
    • More intuitive names, labels and help texts.
  • (E/P) GPU Window:
    • Added the possibility of changing GPU card.
    • GPU status is now linked to on/off preference without waiting.
  • (E/P) Twin Slicer:
    • Frame number and time (seconds) are now shown by default on time series.

Bug fixes

  • (E/P) Communication with Leica's LAS X software:
    • Opening a LIF sub image in Huygens and exporting to Leica results now in more precise meta data.
    • Restore the use of full 16-bits range when exporting to Leica which was briefly disabled in the 16.05.1X version.
  • (E/P) Batch Processor:
    • Fix slow behaviour when listing many files or deconvolution jobs.
  • (E/P) SFP Renderer:
    • Fix several scene inconsistencies.
    • Fix a crash on an image with very many pixels in a single slice.
    • Fix the re-centering of the image after the windows is resized.
  • (E/P) MIP Renderer:
    • Fix the re-centering of the image after the windows is resized.
  • (E/P) File Series tool:
    • Fix launching the Stitcher with only 2 tiles.
  • (E/P) Stitcher:
    • Fix displaying only 1 channel when opening file series.
    • Fix hidden brightness tool with multi channel images.
  • (E/P) Fix potential issue on opening an internet browser from hypertext in Huygens.
  • (All) Histogram:
    • Fix marginal case where the count can be off by 1.

16.10.1p4
(3rd May 2017)
  • Fix regression in Operations Window where the CMLE command did not show input fields for the SNR parameter.
  • Fix regression when changing the acquisition pattern in the stitcher.
  • Fix regression in HuCore and Batch Processor: some parameters could be loaded from the meta data unnecessarily.
  • Fix ND2 3D time-series read as one big z-stack.
  • Fix Nyquist estimation of STED and SPIM images in the Parameter Editor.
  • Improve distance accuracy of tracks in Tracker Analyzer.
16.10.1p3
(16th March 2017)
  • Fix multiple tile selection in the stitcher (Shift + Left mouse click).
  • Fix differences between OP and BP/DW runs due to a missing 'varPsf' option in the deconvolution templates.
  • Fix wrong acquisition pattern tile order when adjusted in stitcher. It is now possible to adjust the acquisition pattern overlap without touching the pattern.
  • Fix error in stabilize scripting command.
  • Improve OME Tiff handling of missing XML tags.
  • Fix incorrect handling of microscopic template in the Stitcher.
  • Fix incorrect number of CUDA cores for NVIDIA's Pascal generation.
  • Show correct scaling factors of CZI images where the factors were not reported.
  • Improve reading of chunk dimensions in VSI reader.
  • Fix regression in HuCore where the parameter confidence levels got replaced by the template parser.
  • Fix conversion of Zeiss light sheet thickness.
16.10.1p2
(22nd February 2017)
  • Improve performance of data transfers between LAS X and Huygens.
  • Fix (potential) bug in the calculation of 5+ channel histograms.
  • Fix (potential) incorrect interpretation of XML files in Stitcher. Improve memory management. Faster flipping and swapping.
  • Support added for Metamorph ND files version 1.0 in the Full file reader option
  • Add scaling factors to HDF5 file reader / writer.
16.10.1p1
(2nd February 2017)
  • Fix saving 2D images as JPEG for HRM tools.
  • Fix ND2 3D time-series read as one big z-stack.
  • Fix floating licenses for HyVolution.
16.10.1p0
(24th January 2017)
  • Fix 'drag&drop' on Linux and Windows.
  • Support for Multi GPU environments in HuCore/HRM.
  • Support for Metamorph ND files (version 2).
  • Update ome-tiff reader for importing more meta data parameters.
  • Fix error in the Windows version of the CZI reader.
  • Fix 'scale if necessary' of 16 bit unsigned integers in CZI reader. Add check for overlap between emission and detection wavelengths.
  • Fix incorrect interpretation of confocal/STED channels in some LIF files.
  • Let HuCore determine a more suitable threshold when creating top SFP's.
16.10.0p9
(12th January 2017)
  • Fix potential error in Decon Express when dealing with ICS files.
  • Fix Batch Processor: divide by zero
  • Fix manual vignetting in Stitcher.
  • Strip '.nd2' suffix from Nikon image names.
  • Fix silent truncation of data if more than 4 GB of data is transferred from, or sometimes to, the GPU in a single copy command.
  • Fix incorrect dimensions in VSI file exported from CellSens.

16.10.0p8
(12th December 2016)
  • Many improvements in the Stitcher: control panel, better support for multi channel XMLs, more intuitive deconvolution, and more.
  • Multi GPU Batch Processor: run jobs in parallel on different GPU cards (requires server option).
  • Prevent problems by disallowing to enable/disable the GPU system or to switch the current GPU device while a computation is in progress.

16.10.0p7
(22nd November 2016)
  • Fix potential crash in GPU deconvolution.
  • Fix error in Object Stabilizer when changing time frame before displacements are computed.
  • Fix hidden 'export to LAS X' when there's an 'H' flag and no 'L' flag in the license.

16.10.0p4
(15th November 2016)
  • Fixes when switching GPU devices: i) Prevent resource leaks; ii) Prevent cached FFT plans from being used on the wrong GPU device.
  • Skip the batch chromatic aberration correction if all vectors are 0.
  • Fix editing chromatic aberration correction vectors in batch mode.
  • Fix 'Check for updates' button in 'Help' menu.
  • Support reading the SPIM excitation direction from Leica LIF files.

16.10.0p3
(2nd November 2016)
  • Fix for RPM packages using CUDA versions older than 8.0.
  • Fix for Windows packages using CUDA 7.5.
  • Report frame scaling factors in Decon Express, Decon Wizard and HyVolution.
  • Close Decon Express windows upon removing the source images.

16.05 Release

Highlights

Huygens Professional & Essential
  • Stitcher:
    • Now available in Huygens Essential as well as in Professional.
    • GPU support.
    • Basic support for custom stitching patterns.
    • Support for TIFF based file series.
  • Cropper:
    • Improved performance.
    • Efficient handling of large images.
  • Twin Slicer:
    • New MIP and Sum projection modes.
    • New Contrast Editor for customized channel visualization; for reporting gamma factors and exporting LUTs.
  • GPU status window: improved diagnostics for trouble shooting
  • SPIM/Light Sheet Deconvolution:


Huygens Professional
  • Plugin system:
    • The system for creating loadable plugins has been rewritten to be more simple, and to support Windows (see Huygens Modules).


Minor changes
  • (All) In Tiff reader:
    • Add support for JPEG compression.
  • (All) In LSM reader:
    • Add LSM 800.
  • (All) In CZI reader:
    • Better handling of multiphoton parameters.
  • (All) in VSI reader:
    • Update to latest file specification.
  • (All) In Imaris writer:
    • Improved handling of single-slice 3D images.
  • (All) In LIF reader:
    • Extract and save the sub image meta data from a LIF collection.
  • (All) On Windows, add support for NUMA processors including all their cores.
  • (All) Workaround for NVIDIA's issue where no processing of specific image geometries is accepted at all by the GPU card.
  • (E/P) Surface Renderer:
    • Add the same render buttons as in the MIP and SFP renderers.
  • (E/P) Chromatic Aberration Corrector:
    • Better performance and more accurate scale and rotation.
  • (E/P) Othogonal Slicer:
    • Remove deprecated version. Enable newest version only.
  • (E/P) MIP renderer and SFP volume renderer
    • Changed the channel selector which enables to switch off channels.
  • (E/P) Deconvolution Wizard:
    • Fix hard error on clicking the 'Cancel' button during deconvolution.
    • Add 'GMLE' algorithm choice to confocal data sets. Skip it on 2D data.
  • (E/P) PSF distiller:
    • Support for SPIM/light-sheet microscopes.
  • (E/P) Object Analyzer:
    • Speed enhancements when analyzing large number of objects.
  • (E/P) Object Stabilizer and Object Tracker:
    • Fix stage-dependent 3D slicing.
  • (E/P) Significant speed enhancement for the median filter on byte and integer image types.
  • (E/P) Improved error reporting of GPU-related problems.
  • (P) Performance Wizard:
    • Limit number of trial threads to the CPU. Skip the GPU where all threads are used.
    • Try the licensed microscopy types only.
  • (E) Add Leica LASX export button.
  • (C) Add on-demand GPU option to deconvolution templates.

Bug fixes

  • (All) In ICS reader:
    • On Windows: reading and writing data sets that are larger than 2GB.
    • On Windows: allow the use of extended characters (such as é) in file and directory names.
    • Several fixes for ICS related crashes and for failures to read/write ICS files.
  • (All) In LIF reader:
    • Fix for reading data generated by Leica´s Live Data mode module.
  • (All) In ND2 reader:
    • Fix hard error on specific data.
    • Fix potential memory corruption.
  • (All) In Ome writer:
    • Large images are written correctly.
  • (All) MultiMIP yields more consistent results when single-slice images are used.
  • (All) Delayed event handling has been improved such that potential problems are prevented when Huygens is closed.
  • (All) Fix regression in histogram command.
  • (All) On Windows, fix potentially incorrect System IDs which encode 0 cores and lead to astray image processing.
  • (E/P) In Batch Processor:
    • Fix interpretation of 'varPsf' option.
  • (E/P) In GPU QMLE, fix display of deconvolved result.
  • (E/P) In Plot Profile Tool:
    • Fix far from centered default profile.
  • (E/P) In Plot Flux Tool:
    • Fix grey color palette.
  • (E/P) In File Series Tool:
    • Fix error when clicking 'Load Selection' on just one file.
  • (E/P) In Stitcher:
    • Fix zoom jumps.
  • (E/P) In MIP renderer:
    • Fix incorrect verbosity level leading to multiple questions.
  • (E/P) in Surface Renderer:
    • Fix rendering artifacts on extreme large zoom factors.
    • Fix default movie preset.
  • (E/P) Fix incorrect busy state on opening an unsupported file.
  • (E/P) Stabilizer: fix crash on very unstable images.
  • (T) Indexer logs from Titan do not consume as much disk space anymore.



15.10 Release

Highlights

  • GPU acceleration of all major deconvolution algorithms. More info here. Installation instructions can be found here.
  • Improved deconvolution of SPIM data.
  • New LIF reader (Leica) is faster, uses much less memory, and reads recently introduced microscopic parameters.
  • Improved floating license option More info here

Huygens Professional & Essential
  • Object Tracker and Object Stabilizer: new embedded Orthogonal Slicer.
  • MIP Renderer:
    • Support for complex type images.
    • Support for much larger image volumes.
    • Performance and quality improvements in the high quality mode.

Huygens Professional
  • Stitcher:
    • Support for TIFF files and XML layouts.
    • New "Flip & Swap" for changing the layout orientation.

Huygens Titan
  • Streamlined main window:
    • First usage help page.
    • Clear distinction between Projects and Annotations.
  • Additional Tabs:
    • To monitor Titan's activity.
    • View the state of removable drives.
  • Improved responsivity under load.

Minor changes
  • (All) In deconvolution algorithms:
    • Report bleaching factors per slice and per frame.
  • (All) In LSM reader:
    • Add LSM 780.
  • (All) In HDF5 reader/writer:
    • Add support for SPIM parameters.
  • (All) In ICS reader/writer:
    • Add support for STED parameters.
    • Add support for channels with different microscope types.
  • (All) in Compute Engine:
    • Faster opening of all large files.
    • Performance increase in stat command for byte images.
    • Large performance increase in range command, especially for byte images.
    • Performance increase in hist (histogram) command.
    • Performance increase in cs (copy and stretch) command.
    • Add support in label function for 2D binary images.
  • (E/P) In Parameter Editor:
    • Add embedding media Vectashield and Mowiol.
  • (E/P) In MIP Renderer:
    • Automatically renders when zoomed with the mouse wheel.
    • Higher resolution for the quick mode engaged while dragging.
  • (E/P) In Surface Renderer:
    • More efficient memory usage.
    • Increased height to prevent occlusion of widgets in Movie Maker mode.
  • (E/P) in Renderers:
    • Tilt can now be 360 degrees for all renderers.
  • (All) Improved robustness of Floating License requests.
  • (All) Improved reading of Z-stacks and T-stacks in ND2 files.

Bug fixes
  • (All) in Compute Engine:
    • borderFill for 2D images would clear image.
  • (E/P) In Chromatic Aberration Corrector:
    • Fix estimation of rotation between channels.
  • (E/P) In Object Analyzer:
    • Seed and threshold manipulation with keyboard now also added to history.
  • (E/P) In Colocalization Analyzer:
    • Don't allocate too much RAM when computing coefficients with a mask.
  • (E/P) In SFP Renderer:
    • Fix potential overflow on the number of voxels.
  • (E/P) In MIP Renderer:
    • Show the displayed frame correctly:
  • (E/P) In Surface Renderer / Object Analyzer:
    • Fix display of binary images.
    • Fix potential artifacts in integer images when the selected threshold is also an integer.
  • (E/P) In Object Analyzer:
    • Fix position of loaded ROI.
  • (E/P) In PSF Distiller:
    • Fix potential empty result.
  • (E/P) In Movie Maker:
    • Fix high quality rendering for the MIP and SFP renderers.
    • Fix the preview when the transformation includes a shift.
    • More precise zooming interpolation (fixed stuttering).
  • (All) Fix several small memory leaks in file readers.


15.05 Release

Highlights
  • New CMLE and TM deconvolution algorithms on GPU (on request).
    • Can use brick wise deconvolution to accommodate limited GPU memory.
  • New optical option for light sheet (SPIM) data sets (on request).
    • Computation of SPIM PSFs.
    • Adapted brick layer to deconvolve areas of the image where the light sheet is thicker with different PSFs
All Huygens Products (incl. Titan)
  • New reader for VSI files.
  • New reader for JPEG files.
  • Experimental new reader for Leica LOF and XLIF files.
  • Floating licenses
Huygens Professional & Essential
  • Chromatic Aberration Corrector
    • Replaces the Chromatic Shift Corrector.
    • New improved GUI for better workflow.
    • New correction method which also corrects for rotation and scaling.
  • Deconvolution wizard
    • Improved workflow for template execution.
    • More informative entry page
  • Redesigned Parameter Editor
    • Includes parameter editors embedded in the Batch Processor, Distiller, and Operations Window.
  • New API to exchange images between Huygens and other softwares (available on request).
Huygens Professional
  • Stitching tool
    • Support for TIFF tiles.
    • New options for automatic vignetting correction.
    • Improved performance.
    • More accurate stitching results.
  • SPIM support
  • Convert deconvolution job in Operations Window to template via the Template Editor
  • Extended Tikhonov-Miller deconvolution supporting brick-wise computations and automatic generation of theoretical PSFs.
Huygens Titan
  • Increased freeware indexing limit from 10GB to 200GB
  • Support for JPEGs in image indexer and search results.
  • New searches on:
    • Nyquist compliant images
    • Targets for stabilization and colocalization
    • Image resolution
  • Search improvements
    • Filename search using and/or on multiple keywords
  • Improved activity monitor
  • Preference to set directory for temporary files (thumbnails/database).

Minor changes

  • (All) Improved error messages for img sub commands.
  • (T) In Huygens Titan:
    • Removed redundant version check that slightly impacted indexing performance.
    • Improved error handling when a thumbnail could not be generated due to the memory limit. An 'image too big for now' message is now displayed instead of a generic error message.
    • Notify that an image is not yet indexed in the image metadata area instead of waiting.
  • (E/P) In Deconvolution Wizard:
    • New welcome screen presents an overview of important optical parameters.
    • Removed unused iteration field for qmle algorithm.
    • Improved workflow for the template save stage.
    • Reduced processing time when executing templates.
    • Enabled 'estimate psf' button for STED Channels when using a theoretical PSF.
    • Added "Autocrop" to the template functionality.
  • (E/P) In Gallery:
    • Border is now dependent on image dimensions instead of fixed.
    • Display a black border when #000000 is selected as border color.
  • (E/P) In Template Editor:
    • Better layout (some widgets were obscured).
  • (E/P) In Twin Slicer:
    • Reset view now also resets contrast stretch.
  • (E/P) In Ortho Slicer:
    • Tool can now be closed via the File menu.

Bug fixes

  • (All) In VSI reader:
    • Long file names could be truncated, preventing the files from being opened.
  • (All) In ND2 reader:
    • Long file names could be truncated, preventing the files from being opened.
  • (All) In CZI reader:
    • Huge CZI files could not be loaded in Windows.
  • (All) In "img preOpen" command:
    • Resources could be leaked.
  • (E/P) In Deconvolution Wizard:
    • Some templates would not load PSF.
    • PSF could only be loaded once.
  • (E/P) When using templates the Twin Slicer could not be launched at the last wizard stage.
  • (E/P) In Object Analyzer:
    • ROI could be incorrectly shifted on loading from file.
  • (E/P) In Gallery:
    • Clicking on a slice would not show the slice in the detailed view.
  • (E/P) In Colocalization Analyzer:
    • The analysis could be carried out on a padded image.
  • (E/P) In Surface Renderer:
    • A crash could occur when the MIP and slicer were used from a specific viewpoint.
  • (E/P) In PSF Distiller:
    • The wizard would get into an undefined state if a channel didn't contain any beads.
  • (E/P) In Performance Wizard:
    • The tuning would not be aborted after closing the window.
    • The wizard could not be restarted after closing it from specific window controls.
    • A run would not get started without a confocal flag.
  • (E/P) In Batch Processor:
    • File series where the 'h' of 'Ch' was missing would not be recognized.


14.10 Release (Fall 2014)

Summary
  • New tool: Gallery, view all slices of an image in a tiled view.
  • New functionality: Image feeder, a sort of Dropbox for Huygens.
  • Updated tool: Hot pixel remover, analyze and remove the hot pixels from a raw image.
  • New tool: Performance tuner, tune the amount of cores Huygens uses for image processing.

All Huygens Products
  • Performance optimization of the CMLE deconvolution algorithm and several low level image processing algorithms.
  • GMLE deconvolution: Improved handling of very noisy images, in especially STED and confocal data.
  • Deconvolution reports per channel and frame on the applied background correction.
  • Reader for the new Olympus VSI format.

Huygens Titan
  • Titan uses relaxed criteria when opening very large LIF files. All LIF files are now opened during initial indexing so that Titan knowns the structure of the LIF file immediately.
  • Added 'placeholder' images for very large images that Titan doesn't open during initial indexing. This allows the user to force Titan to generate a thumbnail immediately, even when the current memory limit wouldn't allow the thumbnail generation.
  • Enhanced the way Titan detects series. Titan should now detect even more series, which greatly improves usability and performance.
  • Improved indexing of container formats. Titan now tries to detect the image size of the subimage. This greatly increases the number of sub-images that Titan indexes automatically.

Huygens Professional
  • Stitcher:
    • Added automatic vignetting correction.
    • Improved overall performance and memory usage.
    • Corrected orientation of tiled LIF sub images.

Huygens Essential
  • Activated import/export option with LAS X software.

Minor changes
  • (All) Add support for tiled OME-TIFF files.
  • (All) Renamed term subBrick as varPsf which is more accurate to describe what this option implies.
  • (All) Changed default value of STED saturation factor from 40 to 30 in 'genPsfExpl' command.
  • (E/P) Removed option 'Save as HDF5' from Deconvolution Wizard thumbnails.
  • (E/P) In Deconvolution Wizard do not load the Twin Slicer preferences but use the default ones instead.
  • (P) In Stitcher Wizard do not load the Twin Slicer preferences but use the default ones instead.

Bug fixes
  • (All) In license mechanism: string licenses with no extra flags did not get recognized.
  • (All) In LSM file reader: Emission wavelength was not estimated accurately for low pass and short pass filters.
  • (E/P/C) In Batch processor and HuCore jobs: the sampling distances were not properly loaded from the templates, instead the metadata values were used.
  • (P/S/C) In ICS file writer: data compression was not enabled as intended.
  • (E/P) In Batch Processor: the selected sub image did not get processed. Instead, a different sub image from the same data set was deconvolved.
  • (E/P) In Stabilizer: a license check for Object Analyzer was not needed.
  • (E/P) In Stabilizer: the outliers slider did not behave as intended.
  • (E/P) In Colocalization Analyzer: Huygens could fail to launch the tool.
  • (E/P) In SFP renderer: the scene's aspect ratio and perspective could be wrong depending on the image geometry.
  • (E/P) In thumbnails: a license check meant for Tracker checked on a different option instead.
  • (E/P) In PSF Distiller: an error could be thrown when closing the tool before reaching the last workflow stage.
  • (P) In Stitcher: the normalization of the flat-field image could fail.
  • (P) In Stitcher: the mosaic corners could look a bit too rounded.
  • (T) Search on filename instead of image name in the advanced search.
  • (T) Fixed bug where images with very large metadata fields where not loaded correctly.
  • (T) Fixed bug where searching of path doesn't work in the advanced search.
  • (T) Increased size of annotation comment field.
  • (T) Fixed error where Titan would not go to the correct directory when select 'Find in library tree' in the advanced search tab.

14.06 Release (Spring 2014)

Summary
  • New product Huygens Titan.
  • New stitching option for Huygens Professional.
  • New deconvolution algorithm: GMLE.
  • New sub brick wise deconvolution.

All Huygens Products
New way to handle shape changing PSFs
The shape of PSFs suffering from spherical aberration due to refractive index mismatch is dependent of their depth position in the specimen. Previously this was solved by splitting the image into 'bricks', each with their own PSF. Though efficient, this could give rise to difficult to avoid gluing artifacts. With the new 'sub-brick' method, the Fast Fourier Transform (FFT) based convolution operations which are the heart of all deconvolution algorithms, are replaced by multiple FFTs, each with different PSFs. This new technique is available for the CMLE, QMLE and the new GMLE deconvolution algorithms.
GMLE
The GMLE algorithm is based on the Maximum a Posteriori probability estimation with Good's roughness regularization. It is related to our workhorse CMLE algorithm, but has rapid convergence like the QMLE algorithm. Using the newly developed sub-brick scheme, it is able to deal with shape changing PSFs without resorting to brick-wise processing.
GMLE is by default available for STED data. To use GMLE in the Deconvolution wizard for other imaging modalities 'Expert mode' needs to be switched on.


New product Huygens Titan
  • Indexes all your microscopic images. Titan is a local indexer; you don't need to upload and convert your files to a centralized database, the images and the database stay on your personal computer.
  • Offline index: index your external hard disks and disconnect them. If you want to open an indexed image Titan will tell you on which external hard disk the image is stored.
  • Tag images with texts and group them into Projects.
  • Search in your image database on metadata or annotations.
  • Quickly inspect your image in 5D using the Lightbox image viewer.
  • Open images directly in Huygens Essential or Huygens Professional for deconvolution and analysis.


Huygens Professional - Stitching Option
(contact sales at svi.nl for a test license if you are interested in exploring this option).
  • New, fully automatized stitching option.
  • The stitched scene can be deconvolved while the scene pieces are put together.
  • Vignetting & shading correction is possible upon providing flat field references.
  • Support for CZI and LIF file formats containing information on tile offsets. Support for other formats is underway.

(E/P/C) Batch Processing
  • New 'Autocrop' option allows for conservative cropping of images in batch mode.

Minor changes
  • (All) Support for two level nesting LIF files.
  • (All) The 'preOpen' command returns more information when working with LIF files.
  • (E/P) The STED parameters will be displayed even if no STED license is present.
  • (E/P) Replace ":" with "_" in Deconvolution Wizard results to be more compliant with OS file managers.
  • (E/P) Add LSM 780 to LSM-specific dialog.
  • (All) Skip the STED Z Stabilization (though not the UI option) if the dataset differs too much from vortex STED.
  • (All) Minimize the output of the STED Z Stabilization.
  • (E/P) Change order of 'Skip' and 'Correct' buttons in Z drift stage (Deconvolution Wizard).
  • (C) Add format reports of STED parameters as required by HRM 3.1.
  • (E/P) Adapt texts in Chromatic Shift help, dialogs and reports (Batch Processor only).
  • (All) 'huOpt getFormatInfo' includes the ND2 file format.
  • (E/P) Parameter "Object size" has been renamed as "Penetration Depth" in the SFP renderer.
  • (All) New installer for Mac OS X. Installer removes deprecated binaries that depend on the Aqua toolkit.

Bug fixes
  • (All) Saving with compression was skipped for the target format ics/ids.
  • (E/P) Fix wrong import of the STED 3D parameter when loading old templates in which STED 3D was not present. The default value was wrongly set to 100% whereas it should be 0%.
  • (E/P) Report STED parameters in optical tab.
  • (All) Fix empty result produced by STED deconvolution + measured PSFs.
  • (S) Fix unwanted flip of Y coordinates introduced by Huygens on images provided by MBF Bioscience's clients: 'Stereo Investigator' and 'Neurolucida'.
  • (P) Fix icon selector which failed to show when the Huygens preferences contained stitcher entries.
  • (E/P/C) Fix bug in the 'huOpt' commands which caused the Batch Processor to stall with STED 3D datasets + Stabilization.
  • (E/P) Fix thumbnail menu which (wrongly) grayed out the MIP entry in Freeware mode.
  • (All) Fix ZVI reader which failed to read RGB24 and RGB48 types.
  • (All) Fix memory leaks in STED deconvolution (sub brick mode).
  • (All) Fix in-place and not-in-place stabilization of STED time series (stabilizer tool and "stabilize" command).
  • (All) Fix error in STED deconvolution ocurring when NA > R.I. (lens).
  • (E/P) Fix Twin Slicer time swing.
  • (All) Fix wrong calculation (factor 2) in backprojected pinhole radius (LIF data only).
  • (E/P) Fix a reporting problem in the Batch Processor which hid many statements when the license included the STED + Leica features.
  • (All) Fix memory leaks in the LIF reader.
  • (E/P) Fix 'Done' button which the Deconvolution Wizard missed in a particular (seldom used) route.
  • (E/P) Fix bug in MIP renderer happening when the user chose "Customized Render Size" but provided no customized size.
  • (E/P) Fix wrong background colors in Parameter Editor (Windows Vista and higher).
  • (E/P) Fix brick mode which failed to show the deconvolved results in the corresponding thumbnail (Operations Window and Tcl Shell only).
  • (All) Fix 'unspecified' microscope type when opening OME files.
  • (E/P) Fix timeout issue in Deconvolution template editor. The value was not properly saved for all channels.
  • (E/P) Fix error where Object Analysis results in Colocalization Analyzer could not be saved.

4.5 Release (Fall 2013)


Summary
  • New and improved Orthogonal Slicer (E/P)
  • New Nikon ND2 file importer (E/P)
  • Improved PSF FWHM (Full Width Half Maximum) Analysis tool (E/P)
  • Chromatic Shift Correction made available in Batch Processor (E/P)
  • STED option extended for Leica STED 3X.
  • Improved and extended LIF file reader (E/P)
  • Huygens <-> Leica LAS AF data exchange possibility (E/P)
  • Significant performance and stability improvement for X11 versions of Mac OS 10.7, 10.8, and 10.9 (see also here)

PSF FWHM Estimator
  • (E/P) A tool is added to the PSF distiller to analyse a newly distilled PSF by checking the FWHM of the PSF in all three dimensions.
  • (E/P) Gauss, Lorentzian, Voight and Pearson7 curve fitters have been added.
  • (P) If you have the PSF distiller in your license, the Huygens Professional Analysis menu activates the PSF FWHM Estimator item, to estimate the FWHM (HIW) of already distilled PSFs.

(E/P) Twin Slicer
  • Animation buttons are added to the Twin Slicer next to the time slicers and z slicer. The Animate tab can be used to adjust the number of frames per second.
  • You can reset all viewing parameters to default values in the Twin Slicer, which can be found under View > "Reset view to default".
  • The time-frame sliders in the Twin Slicer now move with discrete steps.
  • Stretch the contrast per screen or globally.

(E/P) Nikon ND2 file importer (Now in Essential and Professional. Expected to be in the HRM per January 2014).
  • This file importer allows Huygens to read Nikon ND2 images. This importer is still considered experimental as metadata extraction is not always read in correctly with certain ND2 file dimensions. We encourage our users to send us their ND2 files and feedback so we can further improve this reader.

(E/P) Ortho Slicer
  • A NEW and improved ortho slicer.
  • More intuitive and easy to use tool.
  • Place the slicer anywhere you want and visualize the slices in all three direction
  • New slicing modes MIP and SUM.
  • Cut thick slices by setting a span
  • Show the corresponding histogram of the selected time frame.
  • Stretch the contrast per screen or globally.

(E/P) STED option
  • Perform deconvolution with images from the latest Leica STED 3X system. STED 3X deconvolution uses a new depth-dependent PSF.

(E/P) Batch Processor
  • The Chromatic Shift Correction is included in the processing workflow of the Batch Processor.

(E/P) Leica software compatibility
  • Improved and extended the LIF XML microscopic parameters parser.
  • Expected in January: Huygens <-> Leica LAS AF data exchange possibility.

(E/P) Deconvolution Wizard
  • Loading deconvolution templates with Chromatic Shift tasks allows the user to choose for chromatic shift correction after deconvolving the image.

(E/P) Colocalization Analyzer
  • Mask visualization in the Colocalization Analyzer.
  • Extended the Colocalization Analyzer to also show the Colocalization Map for 2D images.

(E/P) Object Analyzer
  • The Object Analyzer is extended with a Ripley k-function:
    • When the distance towards the anchor is calculated (a.CMCM), you can request for the clustering around this specific object by right click on the column and select "Ripley k-function".
    • If you want a full cluster analysis (distances of all objects to all objects) the "Full Ripley k-function" shows the k-function of all distances.

(E/P) Object Tracker
  • When slicing through time, tracks in the Track Analyzer now follow the objects for a more intuitive feel.

Minor changes
  • (All) Improvements in the interpretation of CZI meta data.
  • (All) Increased the limit of slices that Huygens can handle in a single dataset from 5000 to 7000 slices.
  • (All) When opening LIF files their XML section will be stored for future reference. This information will be attached to the image when it's saved as HDF5 in Huygens.
  • (All) When opening OME TIFF/OME XML files the meta data provided as XML will be stored for future reference. This information will be attached to the image when it's saved as HDF5 in Huygens.
  • (All) Better pixel conversion when loading unsigned integer CZI images.
  • (All) Added joining and splitting, and statistics and histograms now possible with binary images.
  • (P/S/C) The 'stat' command now also returns the minimum non zero.
  • (P/S/C) Added a command 'solvePGauss' to solve linear systems by using the Gauss-Jordan method. The matrix coefficients must be provided as pixels of a 2D image.
  • (P/S/C) Improved performance of the copy line (cl) and copy part (cp) commands, primarily when performing on very large images.
  • (P/S/C) The 'window' command can place any window type on any position within the image, without limitations of profile or border.
  • (E/P/S) For Mac OS, we will only support now the X11 version. Aqua version will be excluded. For OS 10.7, 10.8, and 10.9 X11 versions a boost in performance and stability has been obtained (see here).
  • (E/P) Channel selector widget with many channels (menu button) now also show the next and previous buttons for quick switching.
  • (E/P) Rearranged the items of the deconvolution menu to fully replicate the deconvolution workflow.
  • (P/S) Improved copy/paste and backspace/delete handling in the Huygens Tcl Scripting shell.
  • (P/S) Syntax highlighting for the command help displayed in the Task Reports of Huygens Professional.

Bug fixes
  • (All) Sometimes the CZI reader failed to read a the pinhole radius and NA properly.
  • (All) Fixed a memory leak causing Huygens to crash when deconvolving extremely large datasets under very specific conditions.
  • (All) The CZI reader could fail to read very large strings of floats in the meta data, which surpassed regular storage and precission.
  • (All) The HDF5 file writer skipped an image if it contained extremely large slices.
  • (P/S/C) The window function sometimes created faulty profiles and/or borders.
  • (P/S/C) The Lanczos interpolation used by the resample, shift, zoom, isosampling, eqsampling and rotate commands was not supposed to create a wrap-around effect. Yet, this occurred when the shift applied to an image was larger than the Lanczos kernel.
  • (P/S/C) MiniMip, hist2Ch en persMip commands are now rejected when the source and destination image are the same instead of creating faulty output.
  • (E/P) 3D previews of psf images were shown black due to their low values.
  • (E/P) Multimip command did not update all three destination images correctly.
  • (E/P) The pinhole spacing was visualized at the pinhole radius parameter in the Optical tab of the main windows.
  • (E/P) The workflow of the Deconvolution Wizard for generic/unspecified microscopes is now properly shown.
  • (E/P) The resulting thumbnail of an FFT looked awkward when sending the result to the source image.
  • (E/P) The Chromatic Shift Corrector blocked the shift vector table until an estimation was carried out. It was actually intended that the user could edit the vectors at any time and correct the image with them.
  • (E/P) The template file dialog appended the extension twice if the user removed the suggested name.
  • (C) The heuristic SNR estimator (version 1.0) could fail when working with highly clipped images.


4.4 Release (Spring 2013)


All Huygens Products
  • Support for the new Zeiss CZI file format in the Full File Format option.
    • CZI files, whether single tiled or multi tiled, can be loaded into Huygens. In the multi tile case the user of Huygens Professional or Huygens Essential will be inquired to select which tiles to open.

Huygens Professional
  • New thumbnails in Huygens Professional. Possibility to show them in 3D and twist/tilt them.
  • The statistics tabs known from Huygens Essential also available in Huygens Professional.
  • New feature to set your own button bar, which is saved in you local preference file. The Icon Selector window can be opened by pressing the grey arrow at the end of the button bar.
  • Used new style icons.

(P) New Icon Selector Window
  • New feature in Huygens Professional to select your own buttons in the button bar.
  • In the icon selector window you can choose all the functionality that can be found in the menu's.
  • With search feature to search for specific functions.
  • Used the new style icons.
  • Extra "Open last" button to open the last opened image.

(E/P) Colocalization Analyzer
  • Extended with a mask option. The mask denotes the area to calculate the colocalization coefficients. The GUI is a little adjusted to hold all the options in a structured manner.
  • The colocalization coefficients are visualized clearly in a table with sorting functionality.
  • The colocalization coefficients choice is stored in your preferences, which means that the last chosen coefficients will be kept.

(E/P) Surface Renderer
  • Included a movie tab similar as in the other renderers (MIP, SFP). In this tab you are able to set more animation settings.
  • Added the seed slider to get the exact same rendering as in the Object Analyzer.

(E/P) Deconvolution wizard
  • New thumbnails also used in the Deconvolution wizard.
  • Added the join channels tool in the last stage of the Deconvolution wizard where you can choose which channels/results to combine in a more intuitive manner.

Minor changes
  • (E/P) New thumbnails also used in the PSF Distiller wizard.
  • (E/P) Added delay feature in the Twin Slicer for the play mode of the slicers, such that you can control how fast the scenes are shown.
  • (E/P/S) The Huygens Software accepts _c of _C in filseries for channel configuration, next to the already accepted _ch, _Ch or _CH convention.
  • (P/S) The resample commands can be applied to time serie images, where the resampling is applied to each time frame.
  • (E/P) The headers and labels in the Microscopic Parameter editor are links to the website giving direct information about a specific parameter.
  • (E/P/C) The 'noMetaData' field is accepted in Batch Processor templates.
  • (E/P) The thumbnail size is stored in you preferences, such that when starting up the software the last chosen thumbnail size is used.
  • (E/P) The Chromatic Shift Corrector can apply more accurate shifts with Lanczos interpolation.
  • (C) The analytic (beta) SNR estimator performs better. Also, the thumbnails of the SNR simulations match better the thumbnails of the sample.
  • (All) Maximum number of images that can be opened in Huygens Software is increased from 500 to 2000.

Bugfixes
  • The Batch Processor yielded slightly different results when executing the same job template. This was due to rounding errors in the FFTW library. This type of error was more exposed when working with the Batch Processor than when working with other tools.
  • Improved the required dependencies for the rpm installation packages, such that installation on CentOS, Suse and Red Hat should perform much better.
  • Improved visualizing histograms in logarithmic scale, where values of 1 are not correctly shown.
  • Removed the blinking of the progress report during deconvolution in Huygens Professional. The progress report is also visible in Huygens Scripting.
  • The Chromatic Shift Corrector failed to load packed images.
  • The dimensions of a RGB zvi format image are set in the correct order.
  • Editing of the tcl shell in Huygens Professional before the command prompt is handled correctly.
  • Fixed an initialization problem seldom seen in the Movie Maker when several renderer types where mixed in the loaded movie maker template.
  • Disabled the Control-t binding in the tcl shell.
  • Used a scroll frame in the cropper, such that widgets that do not fit on screen can be reached with scrolling.
  • Rerendering of the twin slicer scenes when hiding the plot.
  • Opening a tracks file in the Tracker Analyzer which was previously saved with the Object Tracker could throw an error.



4.3 Release (Fall 2012)


(E/P) New Crosstalk Corrector option
  • This new optional tool estimates and corrects channel bleed-through (crosstalk/crossover) for up to 32 different channels automatically.
  • Correction is linear and can be applied interactively using the 2D histogram.
  • Correction values are plotted in a crosstalk coefficient matrix, which can also be manually adjusted.
New batch Colocalization analysis and histograms creation in Huygens Core
  • Added colocalization to the Huygens template readers and task processors. Huygens Core can now compute colocalizaton coefficients and create colocalization maps for pairs of channels in batch mode. A new version of the Huygens Remote Manager will soon be released offering the option to perform colocalization analysis after deconvolution.
  • Added 'histogram' task to the Huygens template readers and task processors. Huygens Core can now create 1D/2D histograms in batch mode.
(E/P) STED
  • Improved LIF support: parse the LIF type for Pulsed, CW non-gated or CW gated STED.
  • Added 'stabilization' stage for STED data to the PSF distiller.
  • Improved SNR control in STED deconvolution.
  • PSF Distiller supports STED data.
  • PSF Distiller estimates STED parameters.
(E/P) Object Tracker
  • New analysis type in the Object Tracker for tracking rotation angle and speed.
  • Implemented saving and loading track data.
  • Possibility to save track detection settings in a template file.
  • Added the Track Analyzer to the main menus and pop-up menus.
  • Tracker works now more robust with small number of samples or time frames.
(E/P) Twin Slicer
  • The line profile within the Twin slicer now updates when slicing through time.
  • Added a channel selector to the basic mode of the Twin slicer and in the view mode in Huygens Essential.
  • Plot more than one intensity line profile at once in the Twin slicer.
  • Remove all arrows and markers from the graph in the Twin Slicer at once, instead of removing them one by one.
  • When creating a new intensity profile it is now possible to plot easily along lines parallel to the axes. This can be achieved by pressing 'Shift' while drawing an arbitrary line with the mouse.
  • Events previously managed with the 'Ctrl' key are now managed with the 'Shift' key. The Ctrl-LeftMouse is now being used to simulate the Middle Mouse button (see also minor changes).
  • The Twin Slicer now shows a "Shortcut Info"-tab explaining all the available shortcuts (key- and mouse-events).
(E/P/S) Usage Report
  • New feature: Usage report tool under the Help menu to visualize and list the use of the different Huygens tools.
Minor changes
  • (All) One-button mice no longer supported.
  • (All) Added possibility to simulate a middle mouse button: 'Ctrl' + 'Left' click.
  • (P) Added convert-tools that already existed in Essential to Huygens Professional. Convert, mirror, flip image, which you can find under Tool > Convert...
  • (P) New button for quick access to the Batch Processor in Huygens Professional.
  • (E/S/C) Report restoration scaling factors. This was only possible in Huygens Professional so far.
  • (E/P) The result file of the Chromatic Shift Corrector is now named "....._aligned" instead of "..... _corrected".
  • Added 'manual' background mode to the Deconvolution Wizard.
  • Backgrounds in byte and integer images are computed with floating point precision. The resulting value is very close to the value obtained by converting the image to floating point prior to background computation.
  • (All) New channel selector widget for easy access and control for viewing different channels.
  • Much reduced memory usage when generating very large PSFs at negligible accuracy loss.
Bug fixes
  • (E/P) The lower threshold slider in the Object Tracker was reset when the upper got enabled and vice versa.
  • (E/P) In the Deconvolution Wizard, the template background values were not displayed or taken into account if the user decided to go through the Wizard stages after loading a template.
  • (E/P) The MIP renderer threw an error when setting 'Custom colors' if the image had more than 4 channels.
  • (All) Applying a negative baseline on byte images, resulted in a wrap around of the negative baseline (e.g. -2 -> 254), which would result in all values to be below zero, which are mapped to 0.
  • Add a fallback value for the socket count: 1. This fixes crash issues with virtual machines.
  • Reading LSM files often led to an unnecessary scaling (division by 2).
  • Files of type ome-xml created with the Bio-formats library could not be opened.


4.2 Release (Spring 2012)


New STED microscope type available in the Huygens suite with astonishing deconvolution results
  • Deconvolution of STED datasets.
  • Extended LIF file reader with STED parameters.
  • New option in the Object Stabilizer to stabilize raw STED data.
  • Batch Processor and the Deconvolution Wizard offer option to stabilize STED raw data.
  • PSF Distiller supports STED data and also estimates STED parameters.
All products
  • Support for very large tiff files (larger than 4 GB, a.k.a BigTiff format). BigTiff uses 64bit offsets.
  • New "invertAndOffset" command.
(P/S/C) More filters and commands
  • New median and percentile filters.
  • New "stabilize" command.
(E/P) New Hot Pixel Remover tool
  • This new tool within Huygens Essential (under Tools) and Huygens Professional (under Deconvolution) is a tool to correct for local high intensities, also known as hot pixels.
  • Strength estimation to automatically determine the hot pixels.
  • Possibility to fine-tune the strength estimation.
  • Correct the image (multiple times if you want to compare different settings), where the hot pixel positions are replaced with the median of its neighbourhood.
  • Combine information in Z, time or channel direction if you have the knowledge that the hot pixels are at the same position in each slice, timeframe and/or channel.
(E/P) Deconvolution Wizard improvements
  • Interactive image comparison and plot tool.
  • Improved embedded Twin Slicer.
(E/P) Colocalization Analyzer
  • Two additional smart background estimators.
(E) Join Images tool
  • The user can now manage and join many images at once.
Minor changes
  • (All): The "thres" and "sthres" commands don't need input for every channel now. Missing channel input will be taken from the threshold value of the last entered channel, instead of using default values.
  • (E/P): The MIP renderer is now backwards compatible and supports old MIP templates.
  • (E/P): Better SFP render efficiency for 2D and 3D (few slices) images.
  • (C): HuCore's Batch Processor now finishes jobs successfully even if the preview generation (SFPs, MIPs, etc) fails.
  • (C): Performance and thumbnail improvements in the beta SNR estimator.
  • (C): HuCore's Batch Processor now accepts empty values in the microscopic templates. Those values, if present, will be fetched from the image metadata, otherwise default values will be used.
Bug fixes
  • (All): Limit memory usage and computation time in generating very large PSFs.
  • (All): Mac OSX Lion: fix memory problems, workarounds for OSX bugs.
  • (All): The Yes/No questions were answered with 'No' if the verbosity level was other than 'normal'.
  • (All): Some OME-TIFF files could not be loaded.
  • (All): R3D images used to be loaded as time series by default.
  • (All): The size of the 'About' window was wrong in some operating systems.
  • (All): The "shift" command underperformed in high quality mode, e.g: multichannel packed images, as opposed to multichannel stacked images, were not shifted.
  • (E/P): The MIP rendering of 2D images did not work in high-quality mode.
  • (E/P): Parsing data for calculating histograms for packed channels is fixed.
  • (E/P): The Batch Processor accumulated channels during the deconvolution.
  • (E/P): Selecting the custom render size in the SFP renderer and rendering afterwards without typing a custom size raised an error.
  • (E/P): The SFP thumbnails would some times appear empty in the Movie Maker.
  • (E/P): An error was raised in the Movie Maker if there was an attempt to render the movie as the preview was being played.
  • (E/P): The MIP renderer did not downsample the image when needed.
  • (E/P): The Movie Maker randomly showed wrong sizes of the MIP thumbnails and previews.
  • (E/P): The MIP renderer raised an error when switching channels if a second instance of the renderer was opened.
  • (E/P): The main canvas of the MIP renderer would often appear off center (only Mac OS).
  • (E/P): A change of the render size in the SFP renderer would lead to the motion mode not working properly.
  • (E/P): In the SFP renderer, 'File' -> 'Save scene' mirrored the scene before saving it.


4.1 Release (Fall 2011)


All products
  • Color pickers frames: In the entire software a new color picker is used which is better-looking and easier to use.
  • A new default color palet is introduced, which is a set of colors that is unambiguous to both color blind people and non-colorblind people.
Operations window in Huygens Pro
  • Microscopic parameters and image processing parameters are located in separate notebook tabs.
  • Improved menu structure.
  • The most frequently used operations can now be accessed through a quick launch button bar.
Maximum Intensity Projection window
  • enhanced MIP renderer, with automatic on-the-fly renders and more parameters for customization.
Object analyzer
  • The watershed segmentation method is added to the segmentation frame. The seed and garbage level work for the watershed as well.
Object Tracker/Stabilizer
  • The cropper version in the tracker and stabilizer is updated.
Object Tracker
  • Region of interest (ROI) selection now possible.
Bug fixes
  • (All) Lif files with a bit-count between 8 and 16 are now also read properly.
  • (All) Improvements when opening images with characters like "[" and "]".
  • (E/P) Removed the automatic focus of canvases which would steal the focus of other windows especially in Microsoft Windows.
  • (E/P) In the object analyzer it is possible to analyse an empty ROI.
  • (E/P) Subimages are now read properly in the batch processor. Only the first subimage was read before.
  • (E/P) The deconvolution wizard now stores all settings in the template such that you can reproduce the deconvolution. (bgRadius) This background radius is now also available in the batch processor.
  • (E/P) Restarting a wizard stage in the deconvolution wizard is improved.
  • (E/P) The SFP renderer did not interpolate several of the parameters when rendering a movie with the embedded movie options.
  • (S) The Huygens topSfp command now works with images that are very small in the z-direction.
  • (C) In Hucore only the first channel of multichannel images was properly deconvolved when using Huygens Batch templates.



4.0 Release (Spring 2011)


BuiltInSlicer.PNG Introduction of a brand new, friendly Huygens Essential user interface
Featuring:
  • A new deconvolution wizard.
  • A step-by-step microscopic parameter wizard.
  • Easy access to important image information.
  • Quick analysis using the embedded slicer.
  • Scalable image thumbnails with individual color settings.
  • Tool-widgets for quick image conversions
All products
  • Deconvolution is about 20% faster as compared to version 3.7.0.
  • Enhanced, faster SFP renderer.
  • Enhanced IntelligentCropper is more powerful and easier in use.
  • Introduced OME TIFF reader.
(C) HuygensCore
  • HuygensCore now supports batch templates which results in a major improvement for the online batch deconvolution tools, such as the Huygens Remote Manager (HRM).
  • These batch templates now support thumbnail generation (SFPs, MIPs, stack movies, time movies and MIP comparisons).
(E/P) ObjectTracker
  • Improved object detection.
  • Detected objects are highlighted using a transparent overlay instead of circles.
  • Filter tracks based on the track length, average speed, etc.
  • Measure Mean Squared Displacements.
  • Create XY, XZ, and YZ velocity scatter plots.
  • Measure 2-point velocities instead of 3-point; this gives more reliable measures in case of random motion.
  • The plots in Track Analyzer and the data in these plots can be exported to respectively .eps and .csv files.
  • Many minor improvements and bug fixes.
(E/P) ObjectStabilizer
  • Enhanced rotation detection.
(E/P) ColocalizationAnalyzer
  • Much improved GUI with tabbed layout
  • Introduction of the RBNCC method (beta).
  • Introduction of the Object Spearman colocalization coefficient.
Minor changes
  • (E/P) The BatchProcessor allows reading meta data from files besides the use of parameter templates during batch deconvolution.
  • (E/P) Improved graphs; measure slopes, enhanced PostScript output.
  • (P/S) Tcl and TclHuygens commands that are entered in the shell become hyperlinks to online documentation.
  • (P/S/C) Enabled jpeg saving of 2D images through Huygens commands.
Bugfixes
  • (All) Fixed some problems in the IPM Tiff reader.
  • (All) Added support for Zeiss LSM files larger than 4Gb.
  • (E/P) Fixed rendering of 2D images with axial sample density 0.
  • (E/P) Fixed creating regions of interest for 2D images in the ObjectAnalyzer.
  • (E/P) Fixed high-quality sub-pixel shift in the ObjectStabilizer.



3.7 Release (Fall 2010)


  • (E/P) New option: Object Tracker (as beta version available - more features will be added soon)
  • (E/P) New option: Chromatic Shift Corrector. This Corrector can estimate and correct for chromatic shifts, fixing the existing misalignments across different channels. The result of this correction is a channel-aligned image free of chromatic shifts. Support for templates is included.
  • (E/P) In the Colocalization Analyzer a magnifier has been included to examine the 2D histogram more closely. Thresholds of 1D histograms, 2D histogram and MIP renderer are all linked and all time frames can be analyzed at once. A new Spearman coefficient is also introduced in the Colocalization Analyzer.
  • (E/P) In the Object Stabilizer, users can now define a spherical 'Regions Of Interest' in the correlation based stabilization mode. Also an improved tracker is available, plus the option to select and remove tracks. New filters are included to remove outliers, noise (high frequencies), and drift (low frequencies) from displacements.
  • (C) A new engine for the Signal to Noise Ratio (SNR) estimator that allows for automatic and accurate SNR determinations of widefield and confocal images of any number of time frames and channels. This new SNR estimator is prepared to work seamlessly with the upcoming release of the Huygens Remote Manager (HRM).

Other changes:
  • (P) In the main window of Huygens Professional, a button bar was added with buttons of functions used most often.
  • (P) The deconvolution template editor has been improved.
  • (E) Templates editor has been updated to store per-channel deconvolution parameters.
  • (P) Beta version of a new deconvolution wizard available.
  • (P) Enabled possibility to save 2D image as JPEG


3.6 Release (Spring 2010)


  • The Huygens Professional now contains a new microscopic parameter wizard. Parameters which are out of normal range will be highlighted and, if possible, corrected.
  • The Huygens Essential includes now an Ortho-slicer, which is an extra visualization tool that was only present in the Huygens Professional.
  • The Object Analyzer has been renewed and improved. The various manipulation tool sets are better distinguished while analysis choices are made clearer.
  • Exporting of data to MATLAB from the Object Analyzer is included now.
  • The Colocalization Option now includes an extension of the Pearson coefficient. Like in the intersection coefficient, in the computation of the Object Pearson coefficient, pixels close or below the background are partially or fully excluded from the computation. In this way the Object Pearson coefficient is not biased anymore by large background areas.
  • The Object Stabilizer now includes a new option that is meant to stabilize large objects for which cross-correlation did not work due to internal motion.
  • The Batch-processor has further improved its scheduling so that shorter deconvolution runs will be finished sooner.
  • The LIF fileformat has been renewed to allow the use of very large datasets
  • Hyper-thread counting for Intel Core i3, i5, and i7 CPU's is now included. The Huygens Software takes full advantage of hyper-threading and only the 'real' cores are taken into account for the license.
  • Reading sampling distances from Nikon ICS files is now fully compatible to the latest Nikon ICS format.



3.5 Release (Autumn 2009)


  • The brand new option called the 'Object Stabilizer' (currently in beta) to measure and correct for cell motion, thermal drift, shaking, and other types of movement. It can stabilize and align by means of:
    • cross correlation;
    • object tracking;
    • center-of-mass alignment.
  • Optical parameters now also include the coverslip position and the imaging direction for improved handling of spherical aberration, in turn leading to improved deconvolution results.
  • A full HDF5 file format reader and writer, now adopted by the Huygens Software as the native open-source file format for images and PSFs. The new format stores all microscopic meta data read by Huygens and includes tags describing the reliability of the meta data.
  • Many changes on the graphical interface, resulting in a more modern appearance, reflecting the powerful deconvolution, visualization and analysis capabilities.
  • Visualization templates for all our 3D renderers, so you can store your favorite views and reuse them with other datasets.
  • Improvements on the Batch Processor:
    • Quicker creation of LIF sub-image jobs.
    • New options for TIFF format output: scaled or clipped results.
  • The Colocalization Analyzer can export the 3D colocalization map as an image, or as a new channel to the original stack. You can later take this map into the Object Analyzer for more complex analysis.
  • The Object Analyzer contains many new features, like:
    • Interactive thresholds setting on the channel histogram
    • Analysis history that you can save, to reproduce the analysis with the same dataset or reuse with other datasets. This also facilitates batch analysis.
    • Undo mechanism, to quickly revert for example an unfortunate object deletion or filtering.
    • Import analysis and visualization conditions from any other open O.A. instance, so that you can replicate them for different datasets.
    • Render all objects with their accompanying numerical label, for easier analysis reference.
    • Reference 3D cube to know the orientation of the dataset even at large zooms.
    • Cropped datasets can be exported as new channels to the original image, not only overwriting the original ones.
    • Optional on-screen tips to guide you.
    • More possibilities for setting the ROI.
    • More possibilities for selecting anchors, also by filtering the objects based on the reported parameters.
    • Discarded objects and selected anchors are remembered, for the current segmentation parameters, when changing frames in a time series or channels in a pipe.
  • Improvements in the SFP renderer:
    • The appearance of the SFP table is now configurable (on/off/mirror).
    • Increased tilt range to 180 degrees, i.e. view from underneath the table.
    • SFP animations are more fluent.
  • The Twin- and Ortho Slicer now support multiple rulers and point markers.

Fixes

  • Fixes in reading the metadata of Leica LIF files.
  • OIF reader updated to support files written with Olympus FluoView 2.x
  • Fixes in reading 16 bit LSM files, and improved metadata parser.
  • Many other bug fixes.

Patch 3.5.1p2

Some important bugs fixed in the file series reader, Batch Processor, scripting commands, and Object Analyzer.

Patch 3.5.0p4

Bugs fixed in the Object Analyzer, deconvolution with many bricks, and others.

Patch 3.5.0p3

Bug fixed in estimating the background.

Patch 3.5.0p2

Some bugs fixed.

Patch 3.5.0p1

  • Essential is able to export microscopic parameters templates again.
  • Reporting of parameters after loading a template in Essential's wizard is more readable now.
  • The coverslip editor doesn't complain when closing anymore.
  • The coverslip position is conveniently updated after cropping the image.
  • STK file reading problem in Huygens Core is now fixed.
  • In Windows, Huygens Professional couldn't save images that contained colons in their names. This is now fixed.
  • In Windows, Huygens could not save files to file servers shared with Samba. This is now fixed.



3.4 release (Spring 2009)


Patch 3.4.0p1

  • Fixed brick artifacts that showed up in confocal images under very large refractive index mismatch, with lens' r.i << medium's r.i.
  • Fix for the Movie Maker to render movies in the Intel Mac OS X 10.4 version.

Release 3.4.0p0

  • A brand new Movie Maker optional module. This tool allows you to easily create sophisticated animations of your multi-channel 3D images using the powerful Huygens Visualization renderers.
  • A HDF5 file format reader.
  • A File Series Tool for data selection within large file series.
  • Histogram analysis for the columns of the Object Analyzer.
  • Speed improvements in the interactivity of the Object Analyzer and the Surface Renderer.
  • Scale bars in the Surface Renderer and Fast Mip renderer.
  • A button for the Surface Renderer to render in high quality mode before saving the image.
  • Enhanced contrast in the overlays in the Twin Slicer and Orthogonal Slicer.
  • Fixes in reading the metadata of Zeiss ZVI and Leica LIF files.
  • Improvementes on the Batch Processor: allowing saving multidirectory single TIFF files and other fixes.
  • Better handling of experimental PSFs in large spherical aberration situations, that previously caused too many bricks.
  • The plot command in Huygens Pro can now plot not only functions of one variable in 2D, but also functions of two variables in 3D.


3.3 release (Fall 2008)


Patch 3.3.2p1

  • The Batch Processor can optionally load a whole file series as a single data set, or just each file separately.
  • Fixed wrong scaling of integer images after deconvolution in certain cases that generated some negative pixels.
  • Fixed slicer pipe in Surface Renderer so that it works with all kinds of data types.
  • Improved column statistics reporting in the Object Analyzer .
  • Better management of too large objects and memory limitations in the Object Analyzer.
  • Implemented new brick modes for the deconvolution commands to handle extreme Spherical Aberrations cases: "one" really forces one brick if memory allows it, "sliceBySlice" goes to the limit of very shallow bricks.
  • OME reader/writer updated to OME v1.0 (2008-09).
  • Fix in reading large Tiff/LSM files (up to 4 GB on 64 bit systems).
  • Fixes in the LIF reader: More reliable way to obtain the sample sizes. Find out if an image is widefield or confocal.
  • Fix to avoid a crash in Linux at start up caused by collision with certain X11 libraries.
  • Fixes in the Batch Processor to let it run in 32 bit PowerPC Macs.
  • Fix in Apple installer for 10.5 to avoid removing the software when re-installing the same version.

Patch 3.3.0p3

  • More bugs fixed after the reports of our kind testers, specially in all the new features listed below
  • Improvements on the calculation speed of the Object Analyzer (specially noticeable with a few thousands of objects) and some other requests

Patch 3.3.0p2

  • Some reported bugs fixed.

Release 3.3.0p1

  • The Object Analyzer now offers many new features: new object properties measurements, object filtering, enhanced ROI selection and colocalization analysis. See Object Analyzer.
  • Totally renewed Twin Slicer. Synchronized slicing in any orientation, integrated ruler and intensity profile measurement. See Twin Slicer Tutorial.
  • Totally renewed Batch Processor. Wizard for task creation, improved handling and editing of templates, support for multi-image files, delayed start timer. Your old templates will be automatically converted. See New Batch Processor Tutorial.
  • Totally new Orthogonal Slicer in the Huygens Professional.
  • Movie making capabilities for the Surface Renderer.
  • New PSF Distiller in Huygens Pro: see New Psf Distiller
  • New ZVI file format reader. This will be provided under a new option, together with Biovision IPL (Windows), Biovision IPM (Mac), Leica LIF, Olympus OIF and Zeiss LSM. The ever increasing number of file-formats and frequent changes in the formats themsleves are taking much time from our developers. Therefore using specialized one-brand-only formats will require an option from now on.
  • Added Kuwahara to the list of already available restoration filters in Huygens Professional.
  • Huygens Professional now has a built-in functions plotter. It can be accessed through the Huygens command 'huOpt plot'.
  • Added Debian packages. There are now 4 Linux distro's: x86_64.rpm, i386.rpm, amd64.deb, and i386.deb.
  • Linux 3.3 version will be 10% faster than the 3.2 version (this applies to all four basics).
  • Plenty of fixed bugs and implemented suggestions from users (thank you for all the feedback!!!)


3.2 release (Spring 2008)


Supported platforms

  • Windows 32 and 64 bit in parallel: Windows NT 4.0, Windows 2000, Windows Server 2003, Windows XP, Windows Vista.
  • Apple Mac OS X 10.4 and 10.5, for Intel and PowerPC processors. 32 and 64 bit versions available.
  • Linux 32 and 64 bit
  • Optional: Itanium and Irix. For these, please Contact Svi.

Patch 3.2.0p7

  • Essential will remember the user defined color configuration along sessions
  • Fixed a bug that made the program not to be aware of new available versions depending of the version number
  • The object analyzer also reports the waist of an object, and the corrected width is used to calculate the aspect ratios.

Release 3.2.0p0

New features

  • FreeSFP can directly export animations to AVI files.
  • The Object Analyzer
    • Next to center of mass (CM) to CM inter object distances, it is now possible to measure the distance of one object's CM to the surface of a second reference object.
    • More information about the objects in your image, e.g. largest width, location and size of bounding box.
    • A new more convenient display of all measured variables and the measurement conditions
    • More accurate measurement of objects composed of only a few voxels.
  • The Colocalization Analyzer:

  • New File Formats:
    • AVI: the Visualization Tools that allow you to create animations can now save them directly to AVI files, apart from still rendering the independent frames as Tiff series.
    • Huygens reads BioVision IPM (.ipm) and Olympus SIS Tiff series.
    • Huygens writes Delta Vision IMSubs (r3d) files.
    • Huygens Core can write JPEG files, facilitating the implementation thumbnails in the Huygens Remote Manager.

  • The Huygens Professional slicer remembers the visualization settings for the next time you open it.
  • Huygens Pro can now open multiple files in one go: multiple selection is enabled by pressing the Control key while clicking on file names in the Open Dialog.


  • The Psf Distiller is now equipped with provisions that will allow the user to specify a reduced size to the final Nipkow PSF in order to use less memory in some limiting cases.
  • The Execution Log file remains open all the time now during the program execution, reducing the interference with other operating system utilities monitoring file changes, like Apple's Spotlight.


Bug fixes

Many bugs were fixed in collaboration with users that kindly provided very valuable feedback (kudos to all!!!). For example:

  • In the new Huygens Pro, recovery of the old capability of saving in TIFF files in a single file. Also MIP commands are included in the visualization operations.
  • Better time out handling in the Batch Processor.
  • A workaround for an Apple compiler bug that generated strange deconvolution results, sometimes, in Macs running MacOS X 10.5.
  • Improvements in the MacOS X interfaces to increase compatibility.
  • A problem in the Batch Processor not properly handling PSF with spaces in the file path.
  • Default values for the Signal To Noise Ratio when deconvolving confocal images is now more realistic.
  • A bug in the Colocalization Analyzer sometimes rendering a MIP on the image with strange colors.
  • Some crashes of the Linux 64 bit version at startup in some machines due to a static linking of the X11 libraries.
  • Visualization of an image with an extremely dim channel rendered black sometimes.
  • Deconvolving severely undersampled confocal images with measured PSFs sometimes resulted in banding artefacts.
  • Edit > Conversions > Data and channel type conversion generated error SubscribeImageCallback.
  • Linking different views in the Pro Slicer failed when the image names were too large.
  • Errors shown in the Essential interface when handling multi-photon images.
  • Some wrong parameter handlings in the Essential wizard when the user goes back to previous steps make the program halt.
  • Fix preventing the Batch processor from processing a length-N file series N times.
  • Other improvements in the supported File Formats.
    • OME now stores the Microscope Type of the image.
    • Fixed problems reading wavelengths in LSM files with one illumination line per acquisition channel.
    • Fixes in the LIF reader. Improved handling of large LIF files.
    • Fix reading Leica numbered Tiff series, it failed when the number of digits in some counter was not 2.


3.1 release (Fall 2007)


Patch 3.1.0p1

  • Fixes to make the Mac version compatible with MacOSX 10.3.
  • Temporary workarounds to make the Mac version compatible with MacOSX 10.5 (until future OS and Frameworks upgrades make these needless).
  • Fix to read very large (> 4 GB) LIF files in 64 bit Windows.
  • Fix to avoid a cyclic error message when the Twin Slicer was left open during a wizard-guided deconvolution.

Release 3.1.0p0

  • After being a 64 bit parallel application for Linux for many years, Huygens will be also available for Windows 64 bit multi core platforms. In 64 bit applications, memory allocation is no longer a problem, no more Not Enough Memory Available messages — provided enough RAM and swap space is available.

  • All operations will be stored in an Image History that can be saved along with the files (in ICSfile Format), as text files or as Tcl Huygens scripts to easily automate tasks. The Batch Processor will also save the image history of each task, so you'll always know how your images were restored.
  • Improved Tcl Shell for Huygens Professional and Huygens Scripting with the possibility of repeating previous commands, retrieving previous outputs, and expanding image names and Tcl commands.
  • Improved usability of the undo mechanism in Huygens Professional.
  • Improvements in Huygens Core to facilitate HRM operations. Load a single file in a enumerated series.
  • Refined bead rejection criteria in the Psf Distiller.
  • When saving to TIFF files you can select between an intensity scaling optimized for visualization purposes (independent channel stretching) or for further analysis (respecting channel ratios, and reporting scaling factors).

  • Other improvements in the supported File Formats.
    • Huygens can read user-chosen subimages in LIF files.
    • Better handling of LIF metadata, support for the latest LIF versions.
    • The OMEfile Format writer is fully OME compliant.
    • Time Series written in multi-directory Numbered Tiff series are recognized as such.
    • More portable TIFF files, using a dpi (dots-per-inch) parameter that no longer equals the actaul microscopic sampling but one more appropriate for visualization and printing.
  • New File Formats:
    • Huygens reads Olympus OIF file series.
    • Huygens reads IPLab IPL files.
    • BioVision IPM TIFF is supported, but not fully tested.


Bug fixes

Many bugs were fixed in collaboration with users that kindly provided very valuable feedback (kudos to all!!!). For example:
  • Some minor but annoying issues in the different user interfaces.
  • File name handling is improved to support spaces and international characters in the Batch Processor too.
  • Fixed a failure when selecting a very detailed ROI in the Object Analyzer.
  • Huygens Essential Interface remained disabled after certain operations.
  • Fixed a problem that prevented the deconvolution of very large Time Series
  • Fixed a bug that occasionally prevented the resampling of an experimental PSF to be used for images with lower sampling density.
  • On multi core machines the Pro Slicer sometimes showed black stripes in the first column of the image


3.0 release (Spring 2007)


Patch 3.0.0p5

  • Fix a bug in the histogram calculator that prevented the Essential Wizard to run with multichannel images

Patch 3.0.0p4

  • Disregard irrelevant error in the event queue that prevented deconvolution of large time series
  • Fix: error in the isovolume calculation in the object analyzer for very small objects
  • Fix a bug in the Pro GUI: Some switches are active by default in the command, but they are marked the other way around in the interface.
  • Fix: Old templates can't be found in the new locations.
  • Fix: some user preferences (like using the Embedded Memory Manager) do not apply at start up.
  • Fix: Essential 'Recent images' list is inactive
  • Fix: Large surface renderings are not possible, they are limited to the canvas size
  • Batch processor microscopic templates: allow multichannel and edition of a task template.
  • Fix: stopping a deconvolution of a large time series doesn't generates an error.
  • Improve background estimation for time series

Patch 3.0.0p3


Patch 3.0.0p1

  • Some last-minute bugs in the interface of the new Pro Slicer are fixed

Release 3.0.0p0

From this version, all Huygens Software is available for all platforms!!! That means that Huygens Professional is fully revised and is from this moment on also available for native Windows and MacOS X (currently only PowerPC, Intel expected soon). Huygens Essential is again further improved.

New functionality

  • Windows and Mac users can now benefit from all the advanced tools in Huygens Professional
  • The Pro interface was totally rewritten, and a new powerful Pro Slicer was implemented
  • The interactive Batch Processor is incorporated in the Pro as well
  • Also the Surface Renderer, Colocalization Analyzer and Object Analyzer options are available under the Pro from now on
  • The fixed-view MIP renderer in the older Pro viewer was replaced by the more capable MIP renderer from Essential
  • Built-in html browser provides help files for all functions in the Pro that take updated information directly from the SVI-wiki
  • Because the sofware is now build natively for Windows it can benefit from multithreading in that platform too, something that until now was only available for other platforms
  • A Preferences window lets the users interactively set some common preferences, like default read/write directories

What was kept and improved

  • The thumbnail image overview area, but with new, sleeker thumbnails, tooltips, and a pop-up menu to launch render windows
  • The Tcl Shell, now equipped with useful keyboard shortcuts like arrow-up to repeat the last command
  • The Task report window. Previously this was combined with the Tcl shell in a tabbed deck; now they are simultaneously visible.
  • The microscopic parameter edit tab of the older Slicer is replaced by a more informative window.
  • The Operations Window, including the new Pro Slicer and the new microscopic parameter edit window.

Fixed bugs

Among other minor bugs, the most noticeable fixes are:

  • A bug in the Sfp Renderer that could make the program crash in certain conditions.
  • A bug in the Psf Distiller that produced random behavior in the interface in certain conditions (manifested as "too large bead radius").
  • A bug in the initialization routine that made the program freeze while automatically checking for updates, if the SVI server was down.
  • A bug in the Batch Processor that prevented the restoration of some DeltaVision files.
  • Some problems in the interface of the Colocalization Analyzer.
  • Difficulties of the Object Analyzer when handling images with empty channels.


2.10 release (Fall 2006)


New functionalities

  • Online help for all the Essential tools. Assistance is also provided in the wizard by text links at the bottom of the info panel. (E)
  • Added import and export deconvolution templates to the wizard. (E)
  • New file formats:

Improvements
  • Changes in the Psf Distiller to better extract beads and calculate cone angles, reducing also the number of questions to the user.
  • The FreeSFP is now included in the Huygens suite and not as an independent distribution.
  • Stability and speed improvement of the cropper tool. (E)
  • Added support for unsigned short datatype in DeltaVision files.
  • Update of the pinhole calculation of Olympus Fluoview Tiff images based on recent reports from the manufacturer.
  • Memory improvements:
    • Reading 16 bit tiff images makes integer images in Essential and Batch processor, reducing the memory needs. Scaling is done only when necessary. New -cmode auto for the img open command.
    • Relax resampling criteria in case of OverSampling and resample using less memory.
    • Reduce memory usage by 10% if internal EMM memory manager is disabled
    • Improved Brick Splitting mechanism for the Mac.

Fixed bugs

  • Bug in the Sfp Renderer that caused artifacts (slices) under certain illumination conditions.
  • Bug in the Psf Distiller occuring when some channels didn't have valid beads (E)
  • Batch Processor (E):
    • Batch tasks are quickly killed after user uses Stop button.
    • Errors concerning the PSF are only reported when they will affect the result.
    • Add date and time tag to the file name in the batch processor when output is in tiff format, to reduce the risk of overwritting.
  • Handle blank images or channels in deconvolution.
  • Improved support for long (up to 128 characters) image names.


Patch release 2.9.1p0 (Summer 2006)

New functionalities


Fixed bugs


Other


2.9 release (Spring 2006)


General

  • File Formats: remote files are now accessed using a more robust buffering method.
  • Reduced memory footprint.
  • Better handling of multichannel LSM images when many channels were acquired simultaneously.
  • Solved bug in exporting the data from user requested histograms.

Huygens Essential


Huygens Professional

  • Fixed a race condition at program termination
  • Many minor bugs solved.

Huygens Scripting

  • New method image borderFill
  • Added shift parameter to image createTransfMatrix
  • Added HSV support to addMipToSurface and chan2rgba


2.8 release (Fall 2005)


  • Adding a microscopical parameters correction window to the Huygens Essential. It can be launched by right-clicking the image, and choosing "Correct Parameters".
  • Adding the ability to address 3 GB on Windows, see our FAQ How can I extend the memory usage on my Windows machine?, to be able to handle much larger image datasets than before on Windows.
  • Adding automatic checks for Huygens updates, and an update check button in the "About" window of the Huygens Essential.
  • Many improvements in the Colocalization Analyzer and Surface Renderer tools.
  • Placing application icons on personal KDE and GNOME desktops.
  • Better channels merging in the Psf Distiller wizard.
  • Using a faster mathematical library from Intel for the Linux distribution.
  • Improving brick-wise restoration of Confocal images with small measured PSF.
  • Adding zooming for oversampled big images in the Huygens Essential wizard.
  • Coloring the geometry entries in light blue and purple in case of OverSampling.
  • Returning the Image Histogram data as Tcl string.
  • File Formats:
    • Adding a new file writer: single multi-layer tiff. The user will be now prompted to choose between exporting his data to a tiff file series, or to a single tiff file.
    • Improving the ICS reader to address larger scopes of channels.
    • Improving the Olympus Fluoview microscopical parameters reading.
    • Improvements in the Multi Channel parameters order of the Zeiss LSM reader.
    • Improvements in file series readers which allow importing larger scopes of numbering schemes.
    • Writing the proper geometry notes in the Biorad files, and improving the 16 bit pic reader and writer.

The contents of previous releases are no longer listed

Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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