RHIZO Tron, image analysis system to analyze minirhizotron images or manually measure scanned roots
Image Analysis for Plant Science
Regent Instruments Inc. since 1991




For sales informations,
contact us by email

WinRHIZO Tron 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: 2015a

Available: 17 November 2015

Bugs fixes:

  • Analysis/Import Traced Roots: Root, Segment and Axis session did not take the session number they were imported to (they retained the session number they were saved from).

Available: 01 July 2015

32-bit & 64-bit versions

  • Can load twice as much images (or larger ones) as previous versions. An error message is now displayed when there is not enough memory to load them.
  • Mutiple images loads 20% more rapidly.
  • Soil depth measurements (minimum, maximum and average) are now available for the image, per Root, Segment and Axis. User can specify depth of tube first location relative to ground surface and the distance or gap between successive locations below it. The depth of each images can be calculated by WinRHIZO Tron or specified by the operator. Because of these new data saved in data files, XLRhizomTron 2015a is required to analyse them. Soil depth at the mouse cursor position is also written in the Information area.
  • .pat files are now replaced by .pa2 files. The new format was required to accommodate new features and measurements of the current and future versions.
  • Gaps modifications:
    • There is a new type of gap region called Depth Gap. It is rectangular but is made for vertical gaps between images (they encompass the whole width from left to right) and the area inside is considered when calculating soil depth (unlike the other types of gap).
    • Gaps can only be defined in an editable analysed region.
    • Gap regions cannot extend beyond an analysed region or overlapp them.
  • At startup, when user chooses Default settings he can now choose between those for a scanner or a camera.
  • Images without analyses can be saved as jpg.
  • It is possible to automatically load a calibration file at startup.
  • When importing paths, existing traced roots in the analysed region are not deleted.
  • Segments can be renumbered using Fitter's convention after adding or deleting nodes.

Interface modifications:

  • Roots and nodes are easier to select. There is a tolerance factor which greatly improves selection of thin nodes.
  • The active segment is more visible (thicker than before).
  • A root can be hidden temporarily (invisible) by pressing a key and bringing the mouse cursor over it.
  • The display of roots' central line can be turned off.
  • The Command Area is larger at startup by default (to display the new depth data).
  • Volume data in the Command Area are written with 4 decimal digits instead of 2, other measurements with 3 instead of 2.
  • Information about the Tube, Location and Session in the Command Area is displayed in one line instead of a few (and is visible even if there are no traced roots).
  • The Gap menu has been renamed Regions (similar to other Regent's products). It holds the Gap and now the Edit Sample Identification commands.
  • By default, Current instead of Previous is active to the right of Load analysis of in Analysis/Parameters. If ICAP is not active, it is inactive (it has no effect).

Bugs fixes:

  • When deleting a segment, in some cases the analysis was not updated.
  • Gaps can be activated by clicking them.
  • Moving the first node of a root, sometimes the first segment was moved.
  • Selecting a root, segment or node with an image selection now updates the Command area data.
  • Paste Region roots and Paste Session roots are only active when they can be pasted (you have selected a region or session different than the one they were copied from).
  • Roots copied from a region and pasted to another can now can be selected and edited as when tracing them. Previous versions (down to 2012) required to select them using an image selection rather than moving the cursor over and clicking them.
  • Segments' identification number is now preserved when copying roots from a region and pasted to another.
  • Roots are not highlighted while mouse button is down (caused the selection red rectangle to disappear and be shown in grey).

Commands/Features removed:

  • Add Root Depth to name (now replaced by real root depth measurements).
  • Color analysis.


  • WinRHIZO Tron 2015a can read older .pat files made with WinRHIZO Tron 2007 or more. If you have files older than this, they must be opened and saved from WinRHIZO Tron2007 to 2014 before they can be read by WinRHIZO Tron 2015a.

64-bit version:

  • 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).

Available: 02 December 2014

Bug fix

  • Import gap regions now updates the analysis as it should (to exclude roots in those regions). With previous versions the user had to define a region interactively (anywhere in the analysed image) to update the analysis after gap regions import.

Available: 17 June 2014

  • The Space-Time traveller now allows for gaps in session numbers (it works with non consecutive numbers which occurs when some sessions are missing).
  • The Space-Time traveller now works with files with less than 3 digits per numbers in ICAP files names (which is not conform to the ICAP naming convention but is used by some root scanners). You can now choose one or the other format but not both at a time.
    • Example of a 3 digits file: ExpName_T001_L001_Date_Time_001_Op.jpg
    • Example of a less than 3 digits file: ExpName_T1_L1_Date_Time_1_Op.jpg
      Both works with WinRHIZO Tron (but the second one is not conform to the ICAP convention).
  • It can batch rotate 90 degrees clockwise (without operator supervision) a series of images stored in a folder. The images are stored in tiff format (not jpg). This new feature is provided because some root scanners save images from top to bottom rather than left to right. The latter is required to display images of a tube one above the other.
  • User can choose to which segments modifications done with Edit Segment Properties applies to. It can be:
    • the active segment only
    • he active segment and those descending from it or
    • the active segment, those descending from it and those ascending up to a fork.
  • Minor display bug fixed in Edit Segment Properties & Edit Root Properties. The blue line icon was not visible.
  • New Magnitude method (same as WinRHIZO Pro, now user has the choice: Standard or Restricted).
  • Segment Number, Order, Magnitude or Path length can be written next to segments over the image.
  • Batch Reanalysis, to reanalyse without operator supervision and with just a few mouse clicks a series of image previously analysed but with different (or same) settings.
  • There are now two methods to number segments; 1) in their creation order (the order in which they have been traced) or 2) Fitter's order (as in WinRHIZO Pro). In the former segments always retain the same number which makes tracking their growth over time easier and in the latter they are numbered in function of their hierarchy.
  • Now support time format with up to 10 letters/numbers (such as "08-15-23-32AM", the limit was 8 before).
  • Free style Gaps created interactively are done faster.
  • A new 64-bit version is now available (as an option at an extra cost). It can analyse larger images and is faster by 1.5 to 10 % compared to the new 2013a 32-bit version. It also has some limitations compared to the latter (inquire for details).
  • In the welcome screen at startup, the user is offered to choose between two settings, those used the last time and the defaults.
  • Data/Data Save Options was renamed Data/Saving Options.
  • Calibration/Method was renamed Calibration/Pixel Size Method. Minor modifications have been done to its design.
  • 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).
  • New App and Acquisition icons.
  • The TWAIN code has been revised to support new scanners and improve existing ones.
  • 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).

Command removed:

  • Display/Channels and sub menu items.

Bug fix:

  • Color analysis: Won't allow for more than 12 color classes per group.

Available: August 10, 2011

  • Root morphology in function of color (length, projected area and number of tips). Color data are saved per image (sum for all roots) and individual root.
  • Gap regions. To skip parts of the image where roots should not be measured such as: 1) when loading a series of image of the same tube at different locations and that part of these images overlap (so that this distance is not measured twice) or 2) when stitching images with no overlap side by side and that roots are not at the same positions in both images (to prevent the gap between the images from been measured in the root length). This command is appropriate when a few roots are to be measured in such areas where no measurements must be made.
  • Gap segments. To skip an area that must not be measured during paths creation. This command is more appropriate for a single or a small number of paths.
  • Modifications to user interaction commands to make it more responsive, efficient (less clicks) and adapted to pen tablet (slate) computers.
  • Support for pen or finger gestures (Flicks).
  • Root, segments and nodes are highlighted when the mouse (pen) cursor is over them to indicate that if you click they will be activated.
  • A node can be activated at the same time as a segment (in one click instead of two).
  • A node can be activated and moved if you click to activate it and hold the mouse button down and drag it.
  • A node, segment, tip and root can be activated (selected) by making an image selection around a node or tip.
  • Root selection and activation are more precise. Roots can be activated by clicking them anywhere in them (rather than close to them).
  • The working mode selectors are larger so they can be selected more easily on smaller screen (tablet).
  • In the Space-time traveler (the window used to load multiple images) you can select the images to load by clicking the icons to the left of the buttons (or the buttons as before).
  • Some minor commands fine tuning.


  • Axis average diameter is no more the average of its segments’ average diameters but the real average diameter of the axis.
  • A new measurement: The number of forks.
  • More data saved in individual ROOT data lines: The number of forks, tips and axis. All tips diameters and living status classification are saved.
  • Can read and handle ICAP files with missing Date and/or Time field.

A new lower cost limited functionality version (called WinRHIZO Tron Mini) has been introduced.

Minor bug fixes.


Available: December 10, 2010

  • The Display of roots names can be turned on/off.
  • The mouse cursor color in the Image Area can be changed.
  • A new command to search for and highlight roots with a specific name or variations of it.
  • The option to Move or Resize roots and nodes faster is back.
  • WinRHIZO Tron will automatically consider root order when resizing a node with two branches so that only segments of the same order are resized (i.e. when resizing the beginning of a segment which is also the beginning of a new order, the brother and father segment nodes diameter are not modified, only the new order segment).
  • The working mode in which roots were traced and edited has been splitted in two. Now there is one for root tracing and one for root edition (node resize, move, add/delete).
  • A new command to remove duplicate roots (identical roots present more than one time) of a region or session (to undo double pastes made by mistake for example).
  • A new command to prefix or append root depth to their name (to get different and unique root names when the same names are used from one location of a tube to another.
  • Image/Acquisition Parameters is back and has the default parameters to use WinRHIZO Tron with the CI-600 root scanner.
  • A new XLRhizoTron 2011, tested under Excel 2010.

Available: March 10, 2009

The previously optional Root Topology Analysis Module (TOPO) is now included in the regular Tron and Tron MF versions at no extra charge. It allows to do manual topology analyses with methods similar to those of WinRHIZO Pro (done automatically in the latter). You can define up to two descending links from each link and specify their hierarchy from which the following information can be extracted;

  • Topological link classification into five categories: EE (External-External), EI (External-Internal), (Internal-Internal), IL (Isolated Link), BL (Base Link).
  • Branching angle (angle between a descending link direction and the direction of the link it is issued from).
  • Link magnitude (number of external links [with a tip] extending from a link.
  • Link path length (number of links between a link and the base link).
  • Link developmental order (primary, secondary, tertiary order...).
  • Root system altitude (largest path length)
  • Root system external path length (sum of path lengths of external links (tip).
  • Axis morphology (length, area, volume of connected links of the same order).

Axis data are no more saved by default, to save them, activate Individual Axis Data in Data/Data Save Options.

The Roots/Delete all roots, and Roots/Delete Active Root commands can be undone.

Roots can be moved with the mouse (in addition to arrow keys while in Region Creation Mode).

Nodes can be moved with the mouse (in addition to arrow keys while in Measurement Mode).

Roots can also be activated in Region Creation Mode (click close to it).

Image loading and saving in tiff files is much faster (±10X).

It can load one more color tiff file format.

It can load wider images in old tiff format.

Image display at low zoom magnifications (1/16, 1/32, Fit) is done much faster (±4X).

The “Fit” zoom magnification will display larger images.

The Copy Active Root, Copy Regions Roots and Copy Session Roots commands are now grouped in a Pop Up menu.

The Paste Active Root, Paste Regions Roots, Paste Session Roots commands are now grouped in a Pop Up menu.

The shift key has the reverse meaning when moving roots with arrow keys. In the previous versions when it was pressed, only the active root was moved while when it was released all roots were moved. Now when it was pressed, all roots are moved and when it is released only the active root is moved.

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.


Available 04 dec 2008

Free to owners of versions 2008 a & b. Sent automatically to registered users.

Bug Fix: When moving or resizing a node with 3 connecting links, only 2 of them were modified.

Interactive command modification: Pressing “Ctrl” and arrow keys will no more resize a node faster, it will instead modify the diameter of only the selected link (not the diameter of all connected links). This will typically be used to change the diameter of a descending link when a new order begins (first link of an axis) without modify the diameter of the links (order) it descends from.


Availability: SEPTEMBER 2008

This is the first version designed 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).

ICAP automatic naming scheme can be used to acquire images from a scanner (or TWAIN compatible camera) and save them to file using that convention. Location number is automatically incremented after each image acquisition. Parameters (current tube, location, session) are saved in the configuration file when you quit Tron and are restored (ready to continue) next time you start the program.

Tron will display a warning message (once) if one or more images do not have the same size when loading more than one image at a time (slice, tile, tube). It will no more crash.

Modification 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.

Modification 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 graphic above the image display status (set with the ShowHide graphic button) is saved and restored at start up.

Automatic image saving after acquisition now done after sample identification instead of right after acquisition

Image/Acquisition Parameters is gone. The TWAIN interface is always active.

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

Some menu items have been renamed:

Display/Information Over Image renamed Display/Image Area

Display/Information in Command Area renamed Display/Command Area

Misc/Print Displayed Image renamed Misc/Print Image Area

The welcome window will fade away after a few seconds.

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

Misc. minor changes to the window interface of a few menu commands.

The information area above the image will display more accurate information about the active calibration (scanner.cal, file, or none) when it is changed or canceled.


Availability: OCTOBER 2006

A New Version for Topology Analyses (TOPO)

This version allows to do manual topology analyses with methods similar to those of WinRHIZO Pro (done automatically in the latter). It is available as an option to WinRHIZO Tron and WinRHIZO Tron MF. You can define up to two descending links (root segments) from each link and specify their hierarchy from which the following information can be extracted;

  • Topological link classification into five categories: EE (External-External), EI (External-Internal), (Internal-Internal), IL (Isolated Link), BL (Base Link).
  • Branching angle (angle between a descending link direction and the direction of the link it is issued from).
  • Link magnitude (number of external links [with a tip] extending from a link.
  • Link path length (number of links between a link and the base link).
  • Link developmental order (primary, secondary, tertiary order...).
  • Root system altitude (largest path length)
  • Root system external path length (sum of path lengths of external links (tip).
  • Axis morphology (length, area, volume of connected links of the same order).

    It is possible to display some of the above classifications over the links in the image using different color schemes.

New features of all versions

  • The Roots/Continue Root command has been renamed Add Descending Segment. This command can be used to prolong an existing root or (for the TOPO version) to make a fork and add a second descending link (brother) to a segment which has already one).
  • The Root/Delete Segment command has been renamed Root/Delete Branch which can now be used to delete a single segment or a segment and all its descendants.
  • Roots can now rollover from one image side to the other (once a root is shifted passed the image boundary it is displayed on the opposite side as if the image was continuous. This feature is for images that come from scanners which scan a 360 field of view in tubes.
  • Tips can be invalidated when the root ending in an image is not the real root end, such as when a segment continues on another image. A symbol (+) is now drawn at each valid tip.
  • There are more image magnifications (zoom factors) and a fit to screen option.
  • The data file format has been modified to accommodate the new data. XLRhizo Tron 2007a is required to analyse files made by WinRHIZO Tron 2007a.
  • It is now simpler and faster to calibrate and analyse an image with roots and a calibration target in the same image. WinRHZO TRON will make the calibration on the displayed image (rather than loading another image).
  • There are now 14 information colors that can be changed instead of 12 in Display/Information Colors.
  • You can specify the RGB values of information colors with numbers from 0 to 255 (in addition to moving the scroll bars).
  • The "Root properties" and "Segment properties" window buttons text is changed when these commands are activated from the menus to validate/edit a root or segment properties (as opposed to when they are displayed during root creation) to display more appropriate actions (Ok continue is replaced by Ok, Stop is hidden and Cancel node is replaced by Cancel).
  • "Drawing style" paths are no more available.

Bug fixes

  • When continuing a root, the previously active segment is deactivated (the problem happened only when the active segment was not the last of the root).

Availability: March 2005

  • Up to four user-definable observations (such as fungae presence, root color...) can be specified for each image (frame), root or root segment. These observations and can be set even if there are no root in the image. They replace the former user variable.
  • You can display a single color channel (Red, Green or Blue) of an RGB color image. Sometimes the root-background contrasts are higher in one color channel.
  • The global data lines now include the total root length, area, volume, number of tips and average diameter for the dead and gone categories of roots/segments (in addition to those that were present before [alive, alive+dead+gone]).
  • 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.
  • Text size is medium size by default instead of small.
  • Scrollbar thumb works with larger images.
  • The appearance of most windows (dialogs to enter settings) have been redesigned.
  • Camera has been merged with Scanner in Image/Origin.
  • Image acquisition via TWAIN compatible devices is now possible.
  • Flickering when resizing the main window has been removed.
  • About command has been moved to Help menu.
  • Compatible with XLRhizoTron 2005a.
  • Fixed bugs
    • The image dpi is no more asked when analysing images from scanners with the Intrinsic calibration method.
    • The right date and time are displayed on screen when loading more than one session (tube, tile).
Availability: 24 January 2003

  • This version solves a bug of version 2003b in root distribution data in function of diameter when the diameter classes were not equal (when Bohm or Custom classification was used).
Availability: 06 January 2003

  • This version is between 100% to 1000% faster when loading multiple frames and it uses a lot less memory.
  • Tron will now automatically set two new root variables. These are:
    • Birth session: the session number that the root has been interactively created by the operator.
    • Death session: the session number that the root has been declared dead or gone by the operator.
  • You can modify the thickness of the lines used to draw the traced roots, the region frames and the nodes. You can also modify the boldness of the text used.
  • Measurement data per segment are now available. They have a format similar to the individual root data.
  • Analysed regions can be created during image loading or anytime after. This allows you to load tubes more rapidly and look at them before the analysis.
  • You can enter the largest tube, session and location numbers to make files search faster.
  • The maximum number of analysed regions has been increased.
  • Measurement data are now available separately for alive roots and for all roots (alive + dead + gone).
  • If you change the living status of the last segment (the tip) or the first segment, all the root segments are updated to take on the same new living status.
  • Roots/Delete All Roots of Active Region now deletes the region's corresponding pat file and its measurements. Note: The pat file is not deleted if you active Analysis/Cancel Analysis.
  • It is now possible to copy and paste a single root.
  • Longer image tubes can be loaded.
  • The ICAP naming scheme can be turned off.
  • A progress bar is shown during tube loading.
  • It has a new identification logo in the about window.
  • Modifications to the data file format
    • Two new data columns have been added to data files for the new Birth and Death session numbers.
    • Columns have been added to data files to accommodate the measurement data for total and alive root in the global data lines.
    • The data files have one more title line that describes the segment data lines content.
    • The PATH keyword that identifies individual root data lines has been replaced by ROOT.
    • The RHIZO keyword that identifies the data file creator in the first row and column has been replaced by RHIZOTron.
    • This WinRHIZO Basic, Reg, Pro compatible data format has been removed. Only the simplified format remains.
  • Bugs solved
    • The Sample Identification window displays the active analysed region identification rather than the one of the selected image at load time.
    • Tron can now load neighboring images after you have changed the working directory.
    • Measurement data displayed in the command area after Delete All Roots of Active Region has been activated is now zero (it used to display the previous analysis data).
    • Two bugs were fixed in Paste region Roots. The pasted location number was not always exact. The measurements data for the pasted regions were updated only if the region was modified (roots created, deleted or edited).
    • The measurements data after loading paths manually or loading one or more tube were updated only if the region was modified (roots created, deleted or edited).
WinRHIZO Tron & Tron MF 2003a

Availability: December 2002

    • Root surface area, projected area and volume per diameter class is now more precise. While the earlier versions used the class average diameter to calculate the above morphological parameters, the new version uses the exact diameter (and length) of each root sub-segment in each diameter classes.
    • Irrelevant warning messages and windows have been removed from the calibration procedure.
    • The maximum number of roots that can be analysed per region and the maximum number of regions have been increased by an order of magnitude.
    • Analysis/Root Creation Parameters has been renamed Analysis/Parameters.
    • If you load an image while no calibration has been done, the loading process is aborted resulting in the suppression of some useless messages.
    • A command that allows to display only root growth has been added. Earlier versions had a command to highlight growth, the new one can display root growth exclusively by hiding root segments that were not affected in time.
    • The Root Properties window displayed during root tracing has one more button that allows to retain the last node created and stop the tracing process (instead of continuing it).
    • The T-shaped cursor displayed over the image during root creation is more visible (it is in color rather than grey).
    • The color of the text in the command area and the information displayed over the image (roots and regions names, root edges...) can be changed.
    • The manual has been updated and improved.
    • It has a new icon different from the WinRHIZO Basic, Reg and Pro icon.
    • The automatic root number counter (of the automatic naming scheme) is automatically updated per region rather than for the image. The root number suggested by default is always the largest existing root number plus one for a given region.
    • A useless warning message has been removed when the root distribution graphic horizontal scale is changed.
    • Images scanned in dots per cm (instead of dots per inch) are analysed more precisely (a very rare situation as the Tron version is used almost exclusively to analyse images acquired with a camera).
    • Navigation among frames, tiles or tubes via keyboard keys has been removed. You must click the acquisition icon or activate Image/Acquire Image.

    Bugs solved

  • The Sample Identification window now works as expected when the operator modifies the default values displayed. When more than one image is loaded (slice, tile...) the information of this window cannot be edited, it can only be viewed.
  • The root surface area and projected area per diameter class of earlier version was 10 times too large (were in mm instead of cm) and volume 100 times too large. An e-mail had been sent to every earlier version owners to inform them of this problem.
  • Some bugs with tube loading have been removed. In some situations "load next" or "previous" tube didn't worked or used to crash when an image was missing.
  • Some bugs in "per session" analysis mode have been fixed (Tron used to switch to "per frame" occasionally.
  • Modifications has been brought to bmp files created with the Misc/Print commands so that they can be opened by more programs.
  • Root and segment properties of uneditable regions can no more be modified by clicking them in the image.
  • When roots are copied from a region and pasted to a different one, their session, location date and time are updated so that they become those of the region they are pasted to.
XLRhizo Tron

Most recent version: 2003b

Shipping date: January 2003.

  • A new XLRhizo has been done and renamed XLRhizoTron. You must use XLRhizoTron V. 2003b or later to analyse files produced by WinRHIZO Tron 2003b.

Known bugs: None

Compatibility: Can analyse files produced by WinRHIZO Tron & Tron MF