Rootfly is a free, open-source software application to aid researchers in minirhizotron image analysis.  Users can use the software to measure the length, diameter, and color of roots, as well as the birth and death rates.  The software is designed to be easy to use, with a minimal number of mouse clicks needed to perform each operation, and with all the data for an experiment stored in a single RFY file.  Automated image processing algorithms are also included to further reduce the manual intervention required.  Rootfly is released under the GNU General Public License (GPL). 

Screenshot:

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Warning!!! Despite the version number, this software should be considered in beta. Use at your own risk. Some users have complained about losing data, but the problem happens infrequently enough that we have not been able to track down and fix the bug. To minimize the chances of losing your data (or having it become corrupted), it is recommended that you break your dataset into smaller datasets, then frequently double-check whenever you have finished annotating a small dataset that the annotations are indeed preserved in the file. In this manner, any corruptions that occur will be limited to the smaller dataset, and you will lose less work. And of course, save early, save often, and make frequent backups.

• Version 2.0 (latest version)
  • Version 2.0.2 (28 June 2011) -- source code (VC++ 6.0)
    File.Rescan now gets called automatically upon image load; display format cleaned up.  More importantly, when session dates are read from file or found by scanning image directory, their indices are now associated with the session number to cause the dates to be displayed correctly (used to use push_back while ignoring missing dates, which skewed the dates).
  • Version 2.0.1 (19 May 2011)
    Added File.Rescan image directory to allow user to rescan image directory if new images added
  • Version 2.0.0 (20 Jan 2011) -- source code (VC++ 6.0)
    Added Edit.New Root Properties dialog to allow user to set the default color and state for new roots
     
• Version 1.8 (older version)
  • Version 1.8.36 (23 Aug 2010) -- source code (VC++ 6.0)
    Bug fix: export was outputting root information after death date
    'Zoom out' shows previous and next sessions (3x3 display)
    Calibration improvement (manual calibration, large images, average multiple lines)
    Extend endpoint allows multiple clicks to continue extending the root in one operation
    Scaling factor and spin control have been added to make it easier to fine tune the diameter
    A checkbox has been added to the Annotate dialog to reduce the tediousness of annotation
    Bug fix:  Automatic root detection no longer crashes
  • Version 1.8.35 (13 Nov 2009) -- source code (VC++ 6.0)
    Bug fix:  Session dates were being incorrectly read from filenames -- Thanks to Marie Arndal for finding the bug
    Bug fix:  root lifetimes were being incorrectly computed from session dates -- Thanks to John Peterson for finding the bug
  • Version 1.8.34 (19 Oct 2009) -- source code (VC++ 6.0)
    Edit.Copy now allows user to copy just a single root.
  • Version 1.8.33 (25 Sep 2009) -- source code (VC++ 6.0)
    Bug fix:  Files not containing a session/window number in the filename will now get a default session/window number assigned to them.
    (Note:  1.8.33 incorrectly states version 1.8.32 in Help.About, although it correctly states 1.8.33 in file properties)
  • Version 1.8.32 (28 Aug 2009) -- source code (VC++ 6.0)
    Bug fix: 'Delete Point' now works again
    Internal bug fix:  empty condition code
  • Version 1.8.31 (17 June 2009) -- source code (VC++ 6.0)
    Bug fix: application was crashing on right button down
    Now warning user when save fails
    Turned debug logging on during save
    Bug fix: arrow buttons in progress window were being disabled incorrectly; now they are always enabled
    Compiled using MFC in static lib
  • Version 1.8.30 (3 June 2009) -- source code (VC++ 6.0)
    Bug fix: root ids are one-based indices (some functions were creating roots with id 0)
    New bitmaps for zoom buttons
    Turned off autosave functionality
    Help.DebugDisplayRootData now shows all roots in tube
  • Version 1.8.29 (20 May 2009) -- source code (VC++ 6.0)
    Bug fix: no longer writing empty condition codes; new zoom icons
  • Version 1.8.28 (17 Mar 2009) -- source code (VC++ 6.0)
    Annotate button; now compiles using Visual Studio 2008; new cursor for root drawing;
  • Version 1.8.27 (05 Nov 2008) -- source code (VC++ 6.0)
    Simplified interface for CopySession
    Fixed bug:  File.Export was only writing the last tube -- Thanks to John Peterson for finding the bug
    Fixed bug:  diameter in exported file was off by factor of two -- Thanks to Luis Valenzuela for finding the bug
    Fixed bug:  CFileFind was being used incorrectly, thus ignoring the last image of the directory
  • Version 1.8.26 (19 June 2008) -- source code (VC++ 6.0)
    Fixed bug that prevented roots from being displayed in the final window of a tube -- Thanks to John McIntyre for finding the bug; also made minor changes to root detection code
  • Version 1.8.25 (06 May 2008) -- source code (VC++ 6.0)
    Installer; New file version; note that 1.8.25 and later will not open files created by 1.8.18 through 1.8.24; see authors if conversion is necessary
  • Version 1.8.24 (25 Apr 2008) -- source code (VC++ 6.0)
    Autodetect, progress window, zoom
  • Version 1.8.23 (17 Apr 2008) -- source code (VC++ 6.0)
    Internal restructuring
  • Version 1.8.22 (03 Apr 2008) -- source code (VC++ 6.0)
    Fixed more drawing bugs
  • Version 1.8.21 (27 Feb 2008) -- source code (VC++ 6.0)
    Fixed several drawing bugs; now able to move a single root
  • Version 1.8.20 (17 Oct 2007)
    Fixed bug that was causing File.Save to crash when writing session dates -- Thanks to Kevin Kosola for finding the bug
  • Version 1.8.19 (13 Aug 2007)
  • Version 1.8.18 (16 Jul 2007) -- source code (VC++ 6.0)
     
• Version 1.0 (obsolete version)
  • Version 1.0.4 (29 Mar 2007) -- source code (VC++ 6.0)
    'Copy session' dialog box now gives user the option of copying only the current tube and window -- Thanks to Kelby Fite for pointing out the confusion with the previous behavior; also fixed some missing keyboard shortcuts ('copy from previous' and 'copy session')
  • Version 1.0.3 (26 Feb 2007) -- source code (VC++ 6.0)
    Fixed bug:  Now uses Bartz filename to determine the session number -- Thanks to Kelby Fite for finding the bug
  • Version 1.0.2 (27 Oct 2006)
    Fixed bug:  Now experiments can span multiple years -- Thanks to Alex Gershenson for finding the bug
  • Version 1.0.1 (3 Oct 2006)
    Fixed bug in reading directories with spaces
  • Version 1.0 (22 June 2006) -- source code (VC++ 6.0)

On-line help

Project coordinators:

• Stanley T. Birchfield, Electrical and Computer Engineering Department, Clemson University
• Christina E. Wells, Horticulture Department, Clemson University

Development:  https://sourceforge.net/projects/rootfly/