Introduction

  Rootfly: Software for Minirhizotron Image Analysis

Overview

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. Future versions will contain automated image processing algorithms to further reduce the manual intervention required. Rootfly is released under the GNU General Public License (GPL).

Image: Rootfly 1.8.29


Intended Use

Rootfly is intended to be used by researchers who wish to study the nature of roots.  To track root development, a user must specify roots and their length, diameter, color, and code in each minirhizotron image.  However, there are tools, such as automatic root detection and the ability to copy root information between sessions, that will assist in this effort. 

Through the various functions in this software, such as data export, a user can observe root lifespan and growth over a period of time.


Definitions

Requirements

Rootfly expects root images of a project to adhere to common filename conventions.  While the session, window, and tube of each root must be specified in the filename, other parameters, such as experiment, time, and initials may also be given (such as in the image below).  For example, the Bartz ICAP uses the filename format experiment_T[tube #]_L[window #]_[session date]_[time]_[session #]_[initials].jpg.  In Rootfly, this image file format would be equivalent to: [expt]_T[tube]_L[win]_[yyyy.mm.dd]_[time]_[sess]_user].jpg.  In practice, a image file of this format may appear as: EXPERIMENT_T001_L000_2007.05.09_070000_001_CBD.jpg.

When the project image directory is specified, any minirhizotron image not in this format will be ignored.  To learn more about making root images ready for a Rootfly project, review preparing images

Image: Image File Format Parameters



About

Rootfly Version 1.8.29
Copyright (C) 2009 Clemson University

Rootfly is released under the GNU General Public License.
   See www.gnu.org/copyleft/gpl.html for details.

Thanks to the many Clemson students who participated in the development and maintenance of this software.

Portions of the code are copyrighted:
Stan Birchfield

Project coordinators:
  - Christina E. Wells, Horticulture Dept. Clemson University
  - Stan Birchfield, ECE Dept. Clemson University


Copyright © 2005-2009, Clemson University

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