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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 older release information see: WhatsNewArchive.

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.

16.10.1p3

(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.








For older release information see: WhatsNewArchive.