New features on Huygens Software

Huygens 4.1 Release (Fall 2011)

• 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.

• 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.

• enhanced MIP renderer, with automatic on-the-fly renders and more parameters for customization.

• The watershed segmentation method is added to the segmentation frame. The seed and garbage level work for the watershed as well.

• The cropper version in the tracker and stabilizer is updated.

• Region of interest (ROI) selection now possible.

• (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.

Huygens 4.0 Release (Spring 2011)

• 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

• 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.

• 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).

• 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.

• Enhanced rotation detection.

• Much improved GUI with tabbed layout
• Introduction of the RBNCC method (beta).
• Introduction of the Object Spearman colocalization coefficient.

• (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.

• (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.

Huygens 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).

• (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

Huygens 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.

Huygens 3.5 release (Fall 2009)

Patch 3.5.1p2

Patch 3.5.0p4

Patch 3.5.0p3

Patch 3.5.0p2

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.

Release 3.5.0p0

• 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.

Huygens 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.

Huygens 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!!!)

Huygens 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:
  • We've removed the h1 and h2 colocalization coefficients from the Colocalization Analyzer because they were too obscure
  • We added the new intersection coefficients, that may be useful in certain circumstances.

• 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

• 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.

Huygens 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

• 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

Huygens 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

• Embedded Memory Manager improved and enabled for Windows too
• Fix to read some strange formatted LSM files
• Batch Processor bugs fixed:
  • It works in Windows now
  • It works inside the Huygens Professional as well (templates problems fixed)
  • Changing of destination directory fixed

Patch 3.0.0p1

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

Release 3.0.0p0

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

• 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.

Huygens 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:
  • Read and write OME-XML,
  • Read Leica Lif.

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

• Leica LIF File Format reader (beta).

Fixed bugs

• Batch Processor task status report.
• Signal To Noise Ratio for QMLE always ended up as infinite in Batch Processor.
• Modification of template values in task lines.
• Fix in TIFF reader, failing at 4-channel images.
• Fix in ICSfileFormat reader, failing at large history track.
• Minor fix in Pro Image Histogram option

Other

• Report scaling of results in the Huygens Essential and the Batch Processor.

Huygens 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

• Batch Processor, a new tool for automatic deconvolution of multiple images.
• QMLE deconvolution algorithm now available through the Batch Processor.
• Object Analyzer, a new tool for Interactive Analysis.
• Many improvements in the Colocalization Analyzer and Surface Renderer tools. New color schemes. R and G colocalization channels simultaneously MIP rendered, for better data thresholding.
• Recently used images list.
• Automatic background estimation now chooses mode appropriate for Microscope Type.
• Improved the structure of the menus.
• Solved bug that produced results different from HuPro's under certain circumstances.

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

Huygens 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, 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.