WinRHIZO is a complete plant root measurement and analysis systems for agricultural and forestry research.
Image Analysis for Plant Science
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Regent Instruments Inc. since 1991

 

 

WinRHIZO


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root analyais, morphology, arabidopsis  

 

WinRHIZO is regularly updated. Owners are invited to visit this web page regularly for news about updates with the features list. For questions, please contact our sales department at sales@regentinstruments.com

Most recent update: WinRHIZO 2017a
WinRHIZO 2017a

Available: 10 April 2017

  • Supports the new LA2400 scanner third generation (introduced in March 2017).
  • Tennant’s statistical intersect root measurement method is back.
  • Free style Analysed and Exclusion Regions (made with lasso) are faster.
    • Analysed regions without exclusion regions are 5.3 times faster than version 2016 and 20.3 than version 2013.
    • Analysed regions with exclusion regions are 5.5 times faster than version 2016 and 22.7 than version 2013.
    • The coarsiness (resolution) of lasso style regions’ boundary is user selectable, allowing a trade-off between spatial precision and analysis speed.
  • Rectangular analysed regions are 1.6 to 2.7 times faster (than 2013 and 2016).
  • Some commands can retrieve settings of the Active Analysed region for viewing how it was analysed or to apply them to other regions (Root & Background Detection, Debris and Rough Edges Filters).

Modifications to Calibration commands

  • Calibration/Pixel Size Method has been redesigned and has new features:
    • It no more has the option of loading 1 or 2 images for calibration, it is always 1.
  • New Calibration won’t load an image, it will use the image displayed in the Image area.
  • If an analysed image is displayed while Load Calibration is activated, it will be reanalysed with the calibration loaded.
  • The Object of known dimensions calibration method was renamed Scale in Image.

Modifications to the Root Distribution Histogram     

  • Its settings are saved in configuration files.
  • If diameter classes (number or width) are modified while one or more analysed region exists, the Active analysed region will be reanalysed with the new histogram classes.
  • Root & Background Distinction was renamed Root & Background Detection, has been redesigned and has new features:
    • It can retrieve settings of the Active Analysed region for viewing or applying them to other regions.
  • Ask to save image after acquisition (in Analysis/Parameters) has been replaced by Save image before acquiring another and has those three differences from the former:
    • it will save the analysed image weather it comes from a file or scanner,
    • it will be saved after the analysis rather than before,
    • it won’t ask for a name but simply append “An” to the existing name.
  • Images can be automatically zoomed to fit the screen after acquisition.
  • Settings are no more saved in tiff image files when these are saved before the analysis.
  • Consume slightly less memory than version 2016.

Interface modifications:

  • Analysis/Preferences has been renamed Analysis/Parameters.
  • The Command area is wider at start-up to allow the display of more information and data.
  • The Command area’s Icons are larger (to select them more easily on tablets or small screens).
  • Save Original Image (With Analysis...) renamed Save Image (With Analysis...).
  • Image/Save Displayed Image renamed Misc/Export Displayed Image For Other Programs.
  • Image/Save Image Region has been removed.
  • Speed/Memory/Feedbacks names shortened.

 Bug fixes:

  • Misc/Print Whole Image when zoom was not 1.0, region boundary was not drawn correctly.
  • “Zoom to fit” displayed horizontal lines at some magnifications.
WinRHIZO 2016a

Available: 10 October 2015

  • This is the first WinRHIZO version made and tested under Windows 10.
  • The Analysed and Exclusion Regions has been recoded and optimised for speed resulting in significantly faster analyses and commands. Here are the functions / commands affected;
    • The analysis is much faster compared to versions 2012, 2013 and 2015, some examples:
      • 3 analysed regions, 3 exclusion regions: 62 to 70% faster
      • 3 analysed regions, no exclusion region: 50 to 60% faster
      • Whole image, 3 exclusion regions: 23 to 60% faster
      • Whole image, no exclusion region: 0 to 58% faster
    • The right mouse click slider is faster (more responsive).
    • Activating, Moving, Resizing and Analysed region is faster.
    • Color analysis is faster.
  • The Root & Background Distinction command can consider or not exclusion regions (it is much faster in the latter case).
  • The Leaf-Hypocotyl area measurement is more precise (± 1 to 5% instead of ±15%).
  • A Scale can be drawn in the Image area to show the relative size of the image content.
  • Analysed regions exported to a file then imported back will retain their name (instead of having numbers).
  • Existing exclusion regions are no more deleted when importing a new set of exclusion regions.
  • Pressing shift to define just one exclusion region is now possible.
  • The analysis progress bar is displayed in the center of WinRHIZO's main window (to avoid hiding the title bar).
WinRHIZO 2015b

Available: 28 July 2015

Bug fix:

  • A crash, which occured when the following three conditions were met: 1) color analysis was active, 2) root morphology measurement was active and 3) Analysed Regions overlaped.
WinRHIZO 2015a

Available: 09 June 2015

32-bit & 64-bit versions

  • Compatible with Regent's STD scanner of third generation.
  • The Pixels Classification image can now be saved in batch analysis (in addition to the analysed image available in previous versions).
  • Displayed Images (but not analysed images) can now be saved as jpg.

64-bit versions

  • It can now load and save jpg image files.
  • It can now acquire images from 64-bit TWAIN sources (not from 32-bit TWAIN sources).
WinRHIZO 2013f

Available: 28 July 2015

Bug fix:

  • A crash, which occured when the following three conditions were met: 1) color analysis was active, 2) root morphology measurement was active and 3) Analysed Regions overlaped.
WinRHIZO 2013d
  • Added support for the new LA 2400 (11000). Without this modification, a wrong offset was used when scanning with the TPU light (it was scanning partly outside the trays).
WinRHIZO 2013c
  • In the welcome screen at startup, the user is offered to choose between two settings, those used the last time and the defaults. When default is selected he can choose among those for images acquired with a Scanner and those for images acquired with a camera.
  • Minor modifications to all commands to make sure their items are visible (some computers displays text larger which could result in missing letters).
  • BASIC VERSION: Fix a problem with data not displayed in the Command Area (Vol, SA, Avg Diam, NTips, NForks, NXings).
WinRHIZO 2013b
  • Fixes a crash situation at startup when loading analysed images.
WinRHIZO 2013a
  • It can now scan at maximum TPU width with Regen's simple scanning interface (STD4800 scanner).
  • Analyses are faster than version 2012 (21% to 57% faster depending upon if whole image or analysed and exclusions regions are used and their shape).
  • Free style (Lasso) Analysed and Exclusion Rgns created interactively are done faster (does not apply to those loaded from files).
  • A new 64-bit version is now available (as an option at an extra cost). It can analyse larger images and is faster by 7 to 33% compared to the new 2013a 32-bit version. It also has some limitations compared to the latter (inquire for details).
  • There is now a setting that allows to choose a trade-off between analysis speed and memory consumption.
  • Image/Acquisition Parameters has new options for Regent's simple scanning interface:
    • Dust/Particle removal filter
    • Choice of speed vs. higher quality scans (for very thin or pale roots)
    • Sharpen filter
    • Use TWAIN Interface has been renamed Use Scanner Manufacturer Interface (TWAIN).

  • Modifications to the interface (to make it easier for new user).
    • In the welcome screen at startup, the user is offered to choose between two settings, those used the last time and the defaults.
    • Analysis/Measurements has been split in sub-commands. Fractals settings are hidden until you activate Fractal analysis and click a button to edit them in a separate window. Link analysis settings (topology and developmental...) items are hidden until you activate Link analysis and click a button to edit them in as separate window.
    • Some menus commands have been renamed or moved.
    • Analysis menu has been simplified and now contain the most important commands to the analysis.
    • Edit Sample Identification was moved from the Analysis to the Regions menu.
    • Pixels classification was moved up in the Analysis menu just below Measurements (to highlight the fact they are closely related) and renamed Root & Background Distinction (to highlight what this command do in less technical terms).
    • Filters was renamed Debris & Rough Edges Filters and got minor modifications to its design.
    • Data/Data Save Options was renamed Data/Saving Options and its items name slighly modified.
    • "More precise color analysis" option was moved from Analysis/Preferences to Analysis/Measurements.
    • The developemental "Loop in links" warning item was moved from Analysis/Preferences to Analysis/Measurements.
    • Calibration/Method was renamed Calibration/Pixel Size Method minor modifications have been done to its design.
Miscellaneous:
  • New WinRHIZO program and Acquisition icons.
  • Won't ask for image size if TWAIN interface is used.
  • Fractal analysis default image display time is 0 instead of 2 sec (analyses will be faster if user is not aware of its effect).
  • Fractal analysis data saved in files are now with 3 significant digits.
  • Regent's target is not active by default when the Object of known dimensions method is selected in Calibration/Method (now called Calibration/Pixel Size Method).
  • Calibration with the Object of known size method can be done with a single object in one axis only (instead of requiring 2, one for the horizontal and one for the vertical axis).
  • A note about Color Analysis (how to activate it) has been added in Analysis/Measurements.
  • Filtered objects are drawn in pink instead of red.
  • After importing a set of Analysed Regions, they are automatically recreated (if an image is loaded before), there is no more need to activate Recreate.
  • The TWAIN code has been revised to support new scanners and improve existing ones.
Commands removed:
  • Display/Channels and sub menu items.
  • Allow analysis regions overlapp (they always can).
  • Tennant statistical root length method.
  • Analysis/Restart Analysis.
Bug fixes:
  • In Batch/Acquisition Parameters the directory where images are saved now works. Minor modifications to its design.
  • Display of tips, forks & crossings now work when Skeleton is selected in Display/Image Area after a link analysis has been done.
  • Color analysis: Won't allow for more than 12 color classes per group.

WinRHIZO 2012b

  • The display of Color classes, Color groups or Objects color classification is now done by clicking the Color image selector in the Command Area (the displayed image is changed each time you click it).

Bug fixes:

All versions

  • A crash after identifying more than 100 nodules.

Pro and Arabidopsis versions

  • A crash when analysing images when an Area or Length/Width Filter was active and Hypocotyle/Leaf Area was also active (when Distinct objects analysis was NOT active).

Arabidopsis version

  • Wrong link owner number displayed in the Command area (only when Distinct objects analysis was used).
  • A crash that occurred sometimes when clicking an object in the image (only when Distinct objects analysis was used).

WinRHIZO 2012a
Release date: September 10, 2011

  • Analysed regions can be defined closer to each other (there are no more restrictions on the intersection with another region frame) and can also overlap (you choose to allow it or not).
  • (Pro) Root length per color (class and group) is now more precise. The criteria to classify root length in function of color now looks at all colors present on the root diameter rather than simply at the root center. Length is distributed in proportion to those of the colors present.
  • (Pro) Root length distribution per color is now available per diameter class.
  • A default diameter can be specified to be used as the initial displayed circle when a circular analysed region is created (Ex: You can specify a 5 or 9 cm diameter to match the size of your Petri dishes).
  • The mouse cursor (+) color in the image area can be changed so it can be seen more easily under different images content.
  • Minor modifications to Display/Over Image.
  • Minor modifications to Analysis/Preferences.
  • It is now possible to define a few exclusion regions and have the analysis updated only at the end of the last one (rather than after the creation of each one).
  • Modifications to the pixels classification with right mouse button (slider) and the Analysis/Pixels Classification command.
  • The right mouse button (slider) can no more be used before an analysis (use Analysis/Pixels Classification instead).
  • The right mouse button (slider) is effective only on the active Analysed Region.
  • It is now possible to make a few such slider regions and have the analysis updated only at the end of the last one (by pressing shift during their creation and releasing shift at the creation of the last one).
  • Analysis/Pixels Classification will no more modify the analysed image or regions. It is provided to be used before an analysis is done. After an analysis, the slider (right mouse click) command should be used instead.
  • Revised manual.

Bug Fix:

  • Crash when saving the color classes, groups or objects classification image.
WinRHIZO 2009b
Bug Fix: Crash that occurred in batch analysis.

WinRHIZO 2009a
Release date: April 10, 2009

  • Root diameter measurement is more precise.
  • The root distribution histogram’s maximum number of classes has been increased by a factor of 5.
  • Diameter classes have 7 decimal digits (useful for analyses with very small diameter classes (close to the pixel size)).
  • Image loading and saving in tiff files is much faster (±10X).
  • It can load one more color tiff file format.
  • It can load wider (larger) images in old tiff format.
  • Images display at low zoom magnifications (1/16, 1/32, Fit) is done much faster (±4X).
  • Draw skeleton is much faster and works with larger images.
  • The “Fit” zoom magnification will display larger images.
  • Right Click Slider (interactive pixels classification adjustment) is faster and work with larger images.
  • All functions of the program have been revised/modified to ensure they work with very large images produced by high-end very high resolution scanners and digital cameras.
  • It can scan a new image format: bi-level black and white (equivalent to a pixels classified image). The pixels classification is done by the scanner at the scanning stage.
WinRHIZO 2008a

This is the first version designed for and tested under Windows Vista (but it also works under XP). It has been produced by a different compiler (the latest available) and thus has inherited some enhancements of modern tools built-in (increased capacity or limits of some functions related to maximum image size).

Note: The Protection key must be reprogrammed (Pro).

A new Arabidopsis version is now available; it is optimised for individual seedling analysis

The Arabidopsis version has all the features of the Pro version, the new features listed below and in addition it can do objects area, width and height measurements, root topology and developmental analyses separately on more than one root system per analysed region. There is no more needs to make an analysed region per object. Objects are drawn a different color in the analysed image and have their own data lines in measurements data files.

The hypocotyle and leaf length and area (precise at 15%) can be measured separately from roots for young seedlings. The identification of the root-root junctions is an interactive process (you click them). It will also calculate shoot (Hypocotyle+Leaf) to root length and area ratios.

Note 1: Root diameter distribution is not available per object.
Note 2: It will work for non-touching and non-overlapping objects. It can do basic area analysis (for more complex shape analysis see WinCAM, WinSEEDLE or WinFOLIA).

New Features & Modifications to the Analysis

Link Analysis (Pro)

  • Link analysis now displays root segments (links) with all their belonging skeleton pixels instead of a straight line from beginning to ending. This allows to better keeping track of curved segments. Link activation (by clicking them) is also more precise and easier. (Pro)
  • You can choose which of link or axis is selected by mouse clicks (when a developmental analysis has been done). When you click them in the image their corresponding data (link vs. axis) are also displayed in the Command area.
  • WinRHIZO displays a warning when a loop in links has been encountered during a developmental analysis (such as when a branch ends on a link instead of a tip).
  • Optional link data saving is off by default.
  • A missing tip can be added (such as when a branch ends on a link because its tip is under or too close to it).
  • The tolerance to classification of double forks classified as crossing is now adjustable (to reduce or remove false crossings detection).
  • The filtering of EE and EI links smaller than a specified length will now remove associated forks (and merge links) and update the number of tips and their distribution (number) per diameter class.
  • The filtering of isolated links will now update the number of tips and their distribution (number) per diameter class.
  • Link order swapping and set manually will now update (reclassify) descending links order.
  • You can double click a link to set its order manually.

Pre-defined analysed regions. They allow to create with a single command, a specified number of equidistant regions at different vertical positions (soil depth) in an image. The size and distance between these analysed regions are specified by the operator. (Reg & Pro)

When loading tiff images previously analysed and saved from WinRHIZO,

  • The analysis is now loaded by default (in earlier versions it was discarded and you had to turn on their loading).
  • You can load or discard display settings (to use some different from when the image was analysed).

10 to 16 bits per pixel grey levels images are saved in 10 to 16 bits (not 8 as before). (Pro)

Enhanced scanner calibration files. Allow WinRHIZO to support new scanners (with their positioning system with regard to our simple scanning interface) without modifications to it (no need to release a new version to support a new scanner).

Modifications to the interface

The mouse wheel can also be used to scroll the image horizontally (it was working before only in the vertical direction). Press ctrl and roll the mouse wheel to scroll horizontally. Press shift to scroll faster in both directions.

Modifications to the Command Area

  • Its width can be changed interactively.
  • You can right click the mouse in the Command area to set the information displayed there.
  • The number of objects present in the analysed region is written in the command area when; 1) the filtering based on area or length/width ratio is active in Analysis/Filters or an individual analysis is done. In such situations, you can also click an object in the image to get its area written. (Reg & Pro)
  • Fractal analysis data are written with three significant digits instead of two. (Pro)

The histogram display status (set with the Show Hide graphic button) is saved and restored at start up.

The Channel selection commands have been moved from the Image to the Display menu. (Pro)

The Analysis/Measurements command has been redesigned to accommodate new measurements. The Morphology item has been renamed Root morphology.

The Display/Image Area, Display/Command Area and Analysis/Filters commands have been redesigned.

Some menu items have been renamed and grouped into hierarchical menus:

  • Regions/Freeze Set of Analysed Regions renamed Regions/Set of Analysed Regions/Freeze
  • Regions/Recreate Set of Analysed Regions renamed Regions/Set of Analysed Regions/Recreate
  • Regions/Export Set of Analysed Regions renamed Regions/Set of Analysed Regions/Export
  • Regions/Import Set of Analysed Regions renamed Regions/Set of AnalysedRegions/Import
  • Regions/Define an Exclusion Region renamed Regions/Exclusion/Define
  • Regions/Delete Exclusion Region renamed Regions/Exclusion/Delete Active
  • Regions/Delete All Exclusion Region renamed Regions/Exclusion/Delete All
  • Regions/Import Exclusion Regions renamed Regions/Exclusion/Import
  • Regions/Export Exclusion Regions renamed Regions/Exclusion/Export

Will zoom closer to the mouse cursor location if it is in image area when pressing the “-” or “+” keys.

Optional data savings (link and color data) are all inactive by default.

There are now two sizes for the symbol drawn to identify tips, forks and crossings and it is now easier to see them when link analysis is display

WinRHIZO 2007d
  • Total root length is displayed in the Command Area (Basic version)
  • The WinRHIZO's welcome window displayed at startup fades away after a few seconds.

BUG FIX

  • A bug fix in the tiff files loading function (extremely rare case)
WinRHIZO 2007c
  • Crash when using the Area or Length/Width ratio filter.
  • Problem with STD1600 scanner. Cannot select the maximum scan area when Regent positioning system is used. Bug was present in version 2007a, b.
WinRHIZO 2007b
  • Support for new scanners (STD4800, STD600 Rapido, VSA600), some ultra fast, some with dual lenses and other ultra-portable.
  • Information about the Scanner.cal file (if it is effective or not) and the scanner which calibration it contains (Manufacturer, Model and Serial number) is now displayed in Calibration/Method.
  • There are now two commands to save an image, one with the analysis and one without it. The one which saves the image with the analysis only saves the original image while the other can save any displayed image (Pixels classification, Skeleton, Color classes or Color groups).
  • Image/Ask to Save Images After Acquisition has been moved from the Image menu to Analysis/Parameters.
  • Misc./Print Displayed Image has been renamed Print Image Area.
  • 4 more colors can be changed in Display/Text & Analysis Colors.
  • The default color group names are now Background, Healthy and Disease (Pro version).
  • Image/Origin window minor redesign.
WinRHIZO 2007a
  • The analysis can be saved with the image (in standard tiff files). It can automatically be recreated when an image previously analysed and saved to a tiff file from WinRHIZO is loaded. This includes exclusion regions and image edition before the analysis but not modifications done to link analysis or image edition after analysis. All the programs settings can be retrieved from the analysed image or discarded. A new command named Analysis/Preferences has been added to store that setting.
  • A manual nodules counter has been added (Basic, Reg and Pro).
  • The Pixels classification command has been improved. It now displays a histogram of the grey levels and color channels distribution to help select a threshold. It will also display the result of pixels classification from any method, including the Lagarde and the Based on color. The Lagarde method has a new option. It can also be used to modify the classification of an analysed region after or before the analysis.
  • Link analysis (Pro version).
    • There is one more method to classify links (a reverse direction ordering similar to developmental).
    • The number and length of main root, laterals and other orders are saved in the global data line and are written in the command area (when a developmental analysis is done).
    • You can choose the information displayed close to links (link number, order, magnitude and altitude).
    • Altitude and External path length are written in the command area data.
    • There is one more criterion (descending length) for order continuation in developmental analysis.
    • In the developmental analysis, WinRHIZO can apply up to 4 criteria of order continuation and switch among them in the order you specify when one comparison test is equal for descending links.
    • Broken links can be merged.
    • EE and EI links shorter than a specified length can be filtered out.
    • The selected link (which information is displayed in command area) is drawn in bold line. Activation of the next link is done by pressing shift and tab.
    • When link analysis is activated, WinRHIZO will turn on the display of links rather than the skeleton. If developmental analysis is activated, the display of developmental order will be turned on. It will revert to display skeleton if link or developmental analysis is turned off.Link information number display is on by default.
    • The name of some commands of the Developmental menu have been shortened.
  • Exclusion regions
    • They can be exported to and imported from files which allows to apply them on different images over time.
    • You can create them without activating menu commands by pressing the shift key and clicking the image.
    • They can be activated by clicking them and commands can be applied to the active one (delete or export it for example). The active region is draw with a continuous line, the others with a dotted line.
    • Their content has no more influence on the automatic threshold selection.
  • Calibration (for images which come from a camera)
    • It is now simpler and faster to calibrate and analyse an image with roots and a calibration target in the same image. WinRHIZO will make the calibration on the displayed image (rather than loading another image) and it will automatically create an exclusion region around the calibration target. The region remains if the analysis is canceled but can be manually deleted with menu commands.
    • Calibration can be canceled from more situations.
    • Regent's target is selected by default when the Object of known dimensions calibration method is active (in Calibration/Method)
  • Misc.
    • Display/Root Colors & Display/Information Colors
      • Display/Root Colors has been renamed Display/Diameter Classes Colors
      • Display/Information Colors has been renamed Display/Text & Analysis Color
      • There are no more overlap in the colors used by both previous commands (a change done in colors of one won't affect the colors of the other).
      • It is now possible to change the color of most of the written text, the region's frame, exclusion region boundaries, tips, fork crossing marks, the right click feedback color (interactive threshold adjustment with the slider).
      • There are now 14 colors that can be changed instead of 12
      • You can specify the RGB value in numbers from 0 to 255 (in addition to moving the scroll bars).
      • Objects rejected by the filters (area or length to width ratio) can be displayed in red over the image (as in older versions).
    • Display/Information Over Image renamed Display/Image Area.
    • Display/Information In Command Area renamed Display/Command Area.
    • An option to save analysed images during batch analysis (all or a sub-sample of them for a random verification).
    • There are more image zoom magnifications and a fit to screen option.
    • The display of the color classes or color groups image is much faster (10X).
    • Filtered objects (with the area or length/width ratio filters) are now counted in the background group in the color analysis data. They are transferred to a color class of the background color group (of your choice).
    • WinRHIZO will remember the operator name between working sessions.
    • More information is saved in data file (image acquisition device, image file name or the word scanner or camera), and minor modifications (- replaced by space, added some spaces).
    • When creating a circular analysed or exclusion region, you must move it or resize it otherwise the whole image is selected (similar to when the rectangular and lasso tools regions are made). Also valid for right mouse click threshold adjustment (slider).
    • The analysis can be interrupted at more places (during debris filtering) while the progress bar is displayed.
    • Some commands' window style has been redesigned (more compact).
    • When editing the color of a color group (for display purposes), only the parameters that can be changed are now active.
    • Grey levels images with more than 8 bits per pixels (up to 16) can be analysed (Pro version).
    • Right click (slider) threshold selection can be done before the analysis.
    • Analysis/Measurements have more options and the name of some items have been simplified.
    • Color classes specifications and groups name are saved on each global data line and all local data lines containing color data (DEV, AXIS, LINK). This allows to track color classes modifications over time when analysing data files.
    • The global data line now contains the analysed region width and height (which can be used to measure an object width and height).
    • The global data line now contains the diameter classes boundaries.
    • The user manual has been revised and updated significantly.
  • Bugs fixes
    • Calibration with Regent's targets crash in some situations.
    • Crash which occurred when resizing an analysed region from the right side over the image boundary.
    • Minor display bug with Recreate last analysed region (when image was zoomed) the temporary box (rect of the rgn) was drawn at wrong place (used when waiting for mouse click for topology analysis or while sample identification window was displayed).
    • When canceling the analysis, if the right mouse click slider is displayed, it will be hidden and the highlighted pixels will be cleared.
    • Smoothing filter can be applied to color images (previous filter worked only on grey levels images).
    • A bug with axis color data.
    • Crash when editing an image after analysis and no data file is open.
    • All modifications to display colors are now saved in the cfg files.
  • XLRhizo compatibility: Use XLRhizo 2006a or later.
WinRHIZO 2005c (Regular version only)

Bug fix:

In Analysis/Measurements, the diameter setting used was always Reg.

WinRHIZO 2005 b
  • Supports the new LC4800-II scanner.
  • Image colors can be inverted (like a negative film).
  • The Help/About and Image/Acquisition Parameters windows style have been redesigned.
  • Bug fix:
    • Top and bottom additional margins (Image/Acquisition Parameters) works as they should (the problem occurred only with some LC scanners).
WinRHIZO 2005a
Release date: January 10, 2005

 

  • Pixels classification (into root and background) can be modified or specified interactively for regions of any shape or the whole image, after the analysis. The process is very interactive and easy to use (more than the previous Pixel Classifier). Pixels that falls into the root group are drawn a different color over the original image as the pixel classification criteria is modified by moving a slider bar. This function replaces the interactive threshold adjustment that was possible before by making an image selection while the "Alt" key was pressed (followed by - or + key presses to change the threshold) and the Pixel Classifier (both have been removed).
  • Root diameter measurement precision has been increased. User can choose between three different precision settings (the precision has an effect on the analysis time).
  • Analysed regions can be moved in the image.
  • Analysed regions made with the lasso tool can be resized.
  • Sets of analysed regions can be saved to a file for later retrieving and application to other images.
  • The area of the analysed region (of any shape) is now saved in the data. Excluded regions are not counted in that area.
  • Calibration of images from a camera can be done with a single mouse click when Regent's new calibration targets are included in the image.
  • Calibration of images from a camera. More options are available as to how and when calibration is done (manually or automatically after load). Targets used for calibration can be in same image as object to analyse or in separate image.
  • Flickering when resizing the main window has been removed.
  • Scrollbar thumb now works with larger images.
  • When recreating a set of analysed regions, each analysed region of an image will have a sample identification name consisting of the image name plus a suffix made of an underscore "_" and a number starting at 1 and incremented for each region (Ex: Image01.tif_1, Image01.tif_2, Image01.tif_3...).
  • When analysing a set of analysed regions in batch analysis mode, each analysed region of an image will have a sample identification name consisting of the image name plus a suffix made of an underscore "_" and a number starting at 1 and incremented for each region (Ex: Image01.tif_1, Image01.tif_2, Image01.tif_3...).
  • Camera has been merged with Scanner in Image/Origin.
  • Added support for latest scanners sold by Regent (LA2400).
  • Bugs solved
    • In AXIS data lines some segments appeared more than once. The total data per axis was correct.
    • A crash which occurred when pressing the backspace key then clicking to edit the image.
    • A crash when doing a topology analysis on an image with no roots in it (which can happen when a strong filter is applied).
    • A crash which occurred when creating an analysed region close to the top of the image.
  • Compatible with XLRHIZO 2005a.
WinRHIZO 2004 a & b
Availability: June 30, 2004.

Version 2004b (free to owners of 2004a)

  • Global threshold will pickup more roots when used with image selections.
  • Can recreate analysed regions made with the lasso tool or circular after RHIZO is quit and restarted (only rectangular regions were possible before).
  • You can display a single color channel (Red, Green or Blue) of an RGB color image and analyse only that channel. You can also analyse the image in color as before or in true grey levels (calculated from the color components). This new feature is in the Pro version only.
  • Image edition is more precise and a few minor annoyances have been removed (white brush, small brush, image zoom...).
  • You can click the custom selected color for image edition in the command area (lower left corner) to change it (works when the working mode is in Image Edition and that the selected color is the Grey or custom color).
  • Calibration (object of known dimensions) can be done in one or two images.
  • Color/Display Groups Rather Than Classes has been renamed Color/Display Groups.
  • Bug fixes:
    • When topology and/or developmental analysis are active and that more than one analysed region are created, RHIZO now displays the instructions to click the base link at the creation of all analysed regions (previously it displayed the message only for the first region, for the others it waited for the click without displaying the message).
    • Recreate Last Analysed Region is now compatible with topology and developmental analysis (it displays the message to click the base link and it will wait for it).
    • Analysed regions resized manually (by moving the region boundary) can be recreated identical to their final size (in previous versions they were recreated the size they had before the manual resizing).
    • Root segments (links) crossing the top of the image are now analysed in the link analysis
  • Compatible with XLRHIZO 2004a.

Version 2004a

  • Any image used in the analysis can be saved (Pixels Classification Image, Color Classes Image and Color Groups Image).
  • Analysis/Root Background & Color Analysis has been renamed Analysis/Pixels Classification and has been redesigned and simplified
  • TWAIN compatibility with recent cameras and scanners (LC4800) has been added.
  • About command has been moved to Help menu.
  • DPI suggested by default (in Image/Acquisition Parameters) have changed for some scanners.
  • Two minor scanning bugs removed.
  • Dual scan has been removed.
  • New and improved manual.
  • New protection key.
  • Known bugs:
    • Lagarde method does not pick as much root as it should or would crash sometimes. This problem is present only in version 2004a and has been solved in 2004b.
  • Compatible with XLRHIZO 2004a.
WinRHIZO 2003 a & b

Availability: July 31, 2003. Will be sent for free (August 15) to those who still have a valid free update period and to those who purchased a WinRHIZO software in 2003. All other WinRHIZO owners who want to get that new WinRHIZO 2003 update, please contact us to find out about our special price.

Version 2003b (includes all modifications of version 2003a)

  • All versions: Root diameter measurement is more precise. The existing algorithm has been refined by measuring diameter at more angles.
  • Reg & Pro versions: Interpolation is available as an option to further increase the precision of root diameter measurement.

Version 2003a

  • Default scanning parameters for the LC3200 scanner are now compatible with Regent's positioning system.
  • Pro version: Color analysis now calculates the root length per link (segment), order and axis in each color class and group (in LINK, DEV and AXIS data lines).
  • The smoothing filter (that minimize rough bark effects on the analysis) has been redesigned. It is now stronger and the user has control over the intensity.
  • Batch analysis can now analyse a region or a set of regions in addition to the whole image.
  • Reg & Pro versions: The pixel classifier has been added. It allows to:
    • Simultaneously view (side by side) at different magnifications the original image, the pixels classified image (in whole or in part) used for the analysis.
    • To modify the analysis pixels classification in specific regions or for the whole image. The modified classification is also visible in a third image that is displayed for comparison.
    • Update the analysis after modifications have been done to the pixels classified image.
  • The difference in percentage between total root length measured with the Tennant and the WinRHIZO method is written in the command area.
  • Diameter classes are specified with three decimal digits (instead of two).
  • Measurements made on images acquired in dots per cm (rather than dots per inch) from programs not made by Regent Instruments are now more precise.
  • The maximum number of analysed regions has been increased by a factor of ten.
  • The mouse wheel can be used to scroll the image.
  • Modifications have been brought to bmp files created with the Misc/Print commands so that they can be opened by more programs.
  • XLRHIZO compatibility: Use XLRHIZO version 2003a. You can also use version 2001a. If you do so, don't care about the warning message when you open the first data file.

    Bugs solved

  • Root length compensation at root tips where half the root diameter is added to the skeleton (to recover length lost during the skeletonisation process) was added to the first diameter class rather than the real root diameter at the tip. The wrong classification was hardly noticeable for the following reasons:
    • compared to total root length, little length is added at tips (there are not so many tips and the sum of total half diameters is a small value).
    • very often (as is by default) the first diameter class is large enough to encompass most tips diameter. The effect was noticeable mostly when the first class was smaller than one or two pixels.

    WARNING! This version does not support the old HP ScanJet and AGFA Horizon series of scanners.

WinRHIZO 2002c
Shipped: 27 March 2002

  • Support for the LC1600 scanner
  • It can analyse objects with a larger diameter.
  • In order to accommodate new features coming in next versions, some parts of the analysis have been revised (measurements produces the same data). The analysis consume slightly (10%) more memory however.
  • Manual developmental analysis modifications are saved in the data file after each modification.
  • Minor bugs corrected
    • Edit sample identification can now edit the volume of soil. As the volume is changed, the length per volume of soil is updated.
    • Recreate last region now works even if regions are deleted before the last one created.
    • Two wrongs instruction messages have been removed in interactive analysis mode.
    • A warning message introduced in version 2002b has been removed. This message prevented from scanning with the TWAIN interface hidden.
  • XLRHIZO compatibility: Use XLRHIZO version 2001a (don't care about the warning message when you open the first data file).
WinRHIZO 2002b
Shipped: 01 March 2002 (this version has been sent to a very limited group). Version 2002c released a few days after has been sent to everyone eligible.

  • This version solves two minor bugs present in 2002a.
  • During batch analysis, the sample identification window is no more displayed. In version 2002a that window was inappropriately displayed and waited for the operator to click OK to analyse the images.
  • The custom dpi item in Image/Acquisition Parameters is now working properly.
  • The programs informs you when a scanner does not support some functions when its TWAIN interface is hidden (when you use Regent's simple interface).
  • The four suggested dpi buttons in Image/Acquisition Parameters are better adapted to new higher resolution scanners (1600 or more optical dpi).
  • XLRHIZO compatibility: Use XLRHIZO version 2001a (don't care about the warning message when you open the first data file).
WinRHIZO 2002a
Shipped: 21 January 2002.

 

  • Better debris filtering. It can reject objects based on area and shape. For example it can reject round objects but not elongated objects (root segments) that meet your criteria.
  • Images can be printed or saved to a bmp file with or without the analysis marks over them. The graphic above the image can also be included.
  • You can edit an image after it has been analysed to add roots manually. You can choose into which diameter class they are added by clicking the corresponding class in the root distribution graphic above the image. Roots added manually will be the color of its diameter class in the graphic (same as the skeleton image). Note: Added roots by this method will modify the morphology analysis but not the link, topology and fractal analysis. To modify these analyses, the edition must be done before the analysis.
  • The edition brushes are round instead of rectangular.
  • Isolated links (IL) can be rejected from link, topology and developmental analyses.
  • Fractal analysis can be done from the Pixels Classification image (previously called the Threshold image) or the Skeleton image (previously called the Analysed image). Both images are used in the scientific community. The Skeleton image is often used when analysing manually traced roots.
  • You can scan binary images (instead of grey levels or color images) and save up to 20% of scanning and analysis time.
  • Scanned images are no more flipped vertically.
  • The Threshold Image has been renamed Pixels Classification image.
  • The Analysed Image has been renamed Skeleton image.
  • Undo Edition can also be done by pressing the Backspace keyboard key.
  • You can edit with the color of a color class or group or a diameter class color.
  • Text size in command area and over image can be set independently.
  • The frame around analysed regions are easier to see. When analysing whole images a frame is drawn around its boundary.
  • The Regions/Analysed Regions command is gone. To analyse the whole image simply click it, to analyse a sub-region of it (any shape) make a selection instead.
  • You can change the color used to draw the diameter classes (root skeleton and root distribution graphic).
  • Paths are gone and are now exclusively in the RHIZO Tron and the new Tron MF versions. Manual root measurement with paths, has been totally redesigned. They are for mini-RHIZOTRON root measurement. The Tron versions now have unique features not found in any programs that will make your work more productive.
  • Manuals (Introduction, Reference and Installation) have been merged into a single document which contains more illustrations and explanations.
  • XLRHIZO compatibility: Use XLRHIZO version 2001a (don't care about the warning message when you open the first data file).
WinRHIZO 2001a FEATURES
(formerly called version 5.0a)
Shipped: January 2001.

  • This version is for Windows 2000, ME and 98. It does not work under Windows 3.1 or 95.
  • Analyses are approximately twice as fast as with earlier versions (depending on which analyses are active).
  • You can analyze image regions of any shape. In addition to being able to analyze whole images and rectangular areas as before, you can now analyze circular regions (useful for analyzing roots or objects in petri dishes) or regions of irregular shapes made with the lasso tool. This feature is not available in the Basic version.
  • You can measure root length and diameter manually in RHIZOTRON images. This is done interactively by drawing over the roots. Manual root analysis also works with images that do not come from RHIZOTRON.
  • You can edit images with any color of your choice by picking up the color from image.
  • Help information is displayed when the mouse is held over the controls (Tooltips).
  • In addition to Surface area (used for root skin area), Projected area (useful for leaf area measurements) is now available. Both area measurements appear in the root distribution graphic and data files as a function of diameter classes or color groups and classes.
  • Projected area per color group and class is now available in data files in the global data line. All previous color analysis data lines are now optional. This makes RHIZO easier to use as a color area meter.

LINK, TOPOLOGY and DEVELOPMENTAL ANALYSIS

  • You can do a developmental analysis manually. As you click root segments, their order (primary, secondary, tertiary) is identified.
  • A new criteria based on Magnitude, for order continuation has been added for developmental link analysis. Existing criteria have been improved slightly.
  • Link number can be displayed in the image.
  • Link order can be displayed in the image (when a developmental analysis has been done).
  • Color keys are shown in the command area (they identify the colors used to draw links classification or dev. order).
  • When topology is active, rejected links (from the topology analysis) are drawn in magenta (this is true whether the displayed link mode is the classification [EE, II, EI...] or dev. order).

MINOR MODIFICATIONS

  • When recreating a set of analyzed regions, incremental numbers are used as naming convention instead of asking a name for each region (this is faster as you don't have to enter a name for each region).
  • The Analysis/Threshold command has been redesigned and merged with Color/Color Analysis Parameters. It is now called Root/Background and Color analysis.
  • Analysis/Reanalyse image has been renamed Analysis/Restart analysis.
  • Pause before analysis is always on.
  • It can analyze images stored in jpeg or windows bmp files.
  • It can analyze tiff image files with a resolution in dot per centimeter.
  • The computer processor is freed when WinRHIZO is idle.
  • Batch analysis will analyze all images (in any supported format) in a folder (instead of just one format).
  • The maximum number of regions per image has been increased.
  • The quantity and quality of the instruction messages in the command area have been improved.
  • Instructions manuals have been rewritten and improved.
  • There is one more optional data type for color data in Data/Data Save option.
  • A menu, called Interactive has been added. It contains commands for manual developmental roots analysis.
  • A menu, called Path has been added. It contains commands for manual root morphology analysis.
  • If only Tennant analysis is active, Tennant measured values are shown in the command area.
  • Root distribution analysis has been removed. You can get the same function with the Save/Recreate Set of Analyzed Regions.
  • There is one more title line and data types (for interactive manual measurements) in data files.
  • In data files; LINK_AXIS has been renamed AXIS.
  • Some icons and buttons in the command area are now hidden when they cannot be used (they are visible only when the corresponding analysis mode is active).
  • The "About WinRHIZO" window now identifies the version model (Basic, Reg or Pro) running.
  • Some image edition flaws have been eliminated (drawing strokes were temporarily lost after window resize or activation).
WinRHIZO 4.1c
Most recent version: 4.1c

Shipped: 29 May, 2000.

Features of version 4.1c

Shipped: 24 May 2000

This version simply fixes one problems in version 4.0 to 4.1b.

  • Some roots were erroneously classified into the last class of the root distribution graphic. The error was below 1% and is now solved.

Features of version 4.1b

Shipped: 08 May 2000

This version simply fixes two problems in version 4.1a.

  • It eliminates crashes which occurred when roots were truncated by the image boundary. This situation was present in version 4.0 and 4.1a.
  • Excluded regions created after an analysis were not completely removed from the data in the files. Those created before an analysis were correct.

Features of version 4.1a

Shipped: 14 March 2000

Scanning

  • Better integration of the STD1600, STD1600+ and LA1600 scanners. These scanners are now easier to use because it is now possible to hide the TWAIN interface. An updated TWAIN driver (V1.73) is required and will be shipped free to all owners of these scanners. With this new version, you simply select the area of Regent's positioning system and this area is scanned
  • Dual scan is now supported on the STD1600, STD1600+ scanners.
  • The Dual scan setting in Image/Acquisition Parameters is saved and restored at startup.
  • Batch scan is no more limited to 99 images and its incremental naming numbers have three digits for easier alphabetical classification. Instead of IMG1.tif it starts at Img001.tif. Uppercase/Lowercase letters are now user selectable. The underscore (_) is gone (but you can add it manually if you want).

Link analysis (and data files modifications)

  • Link developmental analysis can now identify and analyze connected links, called axis, of any order separately. In earlier versions the connectivity was not used so all links of the same order were averaged together to produce average data per order. The new version saves all links that make an axis on individual data lines (one line per axis per order). Global measurements made on them are also available. All links belonging to the axis are also identified.
  • A fifth title data line has been added to data files for the above link axis analysis.
  • A new data type LINK_AXIS has been added to data files for the above link axis analysis.
  • Link information is always displayed in the command area when a link analysis has been done and the operator clicks a link. In the past Links display had to be activated before.

Color analysis

  • A bug introduced in version 4.0 has been solved. Root length and volume (but not area and tips) per color were not measured when Dependent or Independent regions were used to analyze part of an image.

Misc.

  • The Analysis/Measurements section of the reference manual is more detailed.

Known bugs

  • See version 4.1b.

Features of version 4.0a-b

Shipped: 27 January 2000

Note 1: The letter (a, b, c...) at the beginning of a line indicates in which version the modification was made (a stands for version 4.0a ).

Note 2: Some modifications are listed twice, this is because they encompass two categories.

Analysis (in general)

  • The root overlap compensation algorithm has been modified to more accurately measure very large root segments. In earlier versions, larger roots were under compensated in favor of thinner roots.
  • Data are saved right after the analysis rather than when you click the acquisition icon. If modifications are done to the analysis (like adding an excluded area), data in the file are updated automatically.
  • It is now possible to store and recreate a set of analyzed regions (which can be used to analyze different images). First create the analyzed regions, then activate "Regions/Freeze set of analyzed regions". You can recreate the frozen set of regions in any image loaded after by activating "Regions/Recreate last set of analyzed regions".
  • It is now possible to change a fork to a crossing and vice versa. Push Ctrl and click the fork or crossing (useful for topology analysis).
  • It is now possible to delete the last created excluded region.
  • All diameter measurements are given in millimeters. In earlier versions they were occasionally in cm and at other places in mm. If you use a calibration different than the default intrinsic method, the diameter units will be one tenth (1/10) of the length unit.
  • Image edition (useful for topology analysis) has been added.
  • The maximum number of analyzed regions per image has been increased. 

Link analysis

  • Average link measurements has been added to the global data line.
  • Link analysis summary information is now available per link order in data files (when developmental analysis is active).
  • Links can have up to two brothers and three descendants. The data file format has been modified to accommodate this.
  • Link order (developmental topology) can be changed interactively by pushing Ctrl and Shift and clicking the link to change.
  • Links are numbered and saved according to Dr. Fitter's order (leftmost turn first). 

Color analysis

  • Color classification is more precise (especially for very bright or dark colors).
  • Color length measurement is more precise.
  • Color analysis can be done in batch mode.
  • Root volume per color classes and group is calculated (it was always 0).
  • Surface area and volume is not measured for the background group when method of object separation is based on color. Projected area is measured (this allows to use RHIZO as a general color area meter). 

Data files

  • RHIZO's analysis settings (image resolution, analyzed region position,...) are saved with the measurements in data files.
  • In column A of optional data lines, the "-" character has been replaced by the sample identification name (it is repeated from the global data line).
  • The keyword COLOR has been added to color data lines in data files.
  • There is now 3 more titles lines (for link, developmental and color analysis data) at the beginning of data files (for total of 4 instead of 1).
  • Data/Data save options, allows to choose which optional data to save.
  • Average link measurements have been added to global data line.
  • Link analysis summary information is now available per link order in data files (when developmental analysis is active).
  • The data file format has been modified to accommodate that links now can have up to two brothers and three descendants. 

Batch analysis

  • A problem with batch analysis which sometimes stopped after the first image has been fixed.
  • Batch analysis data are now saved in a data file that the operator choose (name and location) before starting the batch analysis. This allows to analyze images stored on CD-ROMs (which was not possible with earlier versions).
  • Color analysis can be done in batch mode. 

New commands

  • Image/Acquire Image is equivalent to clicking the scanner or disk icon in the command area.
  • Analysis/Reanalyse image. Use it to reanalyze an image without reacquiring it.
  • Text size of information displayed in the command area and over the image can be changed.
  • It is now possible to delete the last created excluded region.
  • Data/Data save options, allows to choose which optional data to save. 

Modifications to existing commands or features

  • Image/Ask to save image after analysis renamed Image/Ask to save image after acquisition. The image is now saved right after its acquisition rather than after the analysis.
  • Dual scan is inactive for scanners that do not support it.
  • The command area is larger.
  • Tennant statistical measurement method can be activated without Regent method. 

Misc.

  • There are new scanning instructions manuals for the STD1600 and LA1600 scanners. They have already been sent to owners of these scanners.
  • Root distribution graphic has a better automatic vertical scale adjustment of major and minor divisions.
  • Calibration units are displayed properly when using the object of know dimension calibration method (which is used with images from cameras).
  • Flickering in the command area under certain circumstances has been eliminated.
  • If you quit RHIZO by the Close box instead of the quit command, data are saved before quitting.
  • The name of independent analyzed regions is displayed in their upper left corner.
  • More colors can be changed with Display/Information color.
  • Some abnormal Windows system resources consumption have been fixed.

Known bugs

  • The analysis stops or crashes if a root crosses the image boundary. It has been solved in version 4.1b (available free to owners of version 4.0 or 4.1a).
MacRHIZO (Macintosh version)
Most recent version: 3.10b

There are no more developments on the Mac version. This old version is still available at a reduced cost. It works unders OS 7 to 9.2.

XLRhizo

FEATURES AND COMPATIBILITY
Most recent version: 2003a

XLRHIZO 2003a
Shipping date: January 2003.

Features:

  • There are no new features. The only difference is the suppression of the warning message if you open a file produced by WinRHIZO 2003 or 2002.

Known bugs: None

Compatibility: Can analyse files produced by WinRHIZO versions 5.0 to 2003a.

XLRHIZO 2001a
Shipping date: May 4, 2001.

Features:

  • Supports the new data format introduced in WinRHIZO 5.0a and WinRHIZO 2001a

Known bugs: None

Compatibility: Can analyse files produced by WinRHIZO versions 5.0 to 2003a