Working with Roots

Creating a New Root

To create a root, use the following steps:

      1. Click the Annotate button if you haven't already to allow the editing of roots.
      2. Select the New Root button , Edit > New Root, or Ctrl + R.
      3. Press and release the left mouse button within the image window at the end of a root to make the first point. 
      4. Move the mouse along the root, creating more points as needed using the method in step 2.  More points are necessary to allow  the root drawing to follow curvatures in the root.
      5. When all the root points have been drawn, press and release the left mouse button twice (double-click).
      6. A circle graphic which represents the diameter will appear on the root.  Move the mouse cursor along the root to move the diameter until the desired diameter-drawing area has been reached. 
      7. Press and release the left mouse button to drop the diameter at this point.
      8. The diameter length can now be set.  Move the mouse cursor away from the root to increase the diameter length; move the cursor closer to the root to decrease its length.
      9. Once the desired diameter is achieved, press and release the left mouse button to finish the root drawing.



Select a Root


Once a root has been draw on an image, it can be selected by pressing and releasing the left mouse button anywhere along the drawing.  Once selected, the root's points will be visible, and the root line will be enlarged.


Adding a Point


Use the following steps to add a root point:

    1. Select the root which to add a point.
    2. Move the mouse cursor along the root to where the new point is to be added.
    3. Press and release the right mouse button.
    4. The following option will display next to the cursor: .  Click "Add Point".
    5. A point will be added and it will follow the mouse cursor.  Move the point to the desired location.
    6. Press and release the left mouse button.



Deleting a Point


Use the following steps to delete a root point:

    1. Select the root which to delete a point.
    2. Move the mouse cursor along the root to the point being deleted.  The mouse cursor will change to indicate that it is over a point.
    3. Press and release the right mouse button.
    4. The following option will display next to the cursor: .  Click "Delete Point".



Extending a Root

"Extending" a root will add a point to the end of the root.  This point can be placed anywhere within the image, therefore extending the root's length.

Use the following steps to extend an endpoint:

    1. Select the root which to extend.
    2. Select the Extend Endpoint Button , Edit > Extend Endpoint, or Ctrl + E.
    3. As the mouse is moved into the imagine window, a line will be drawn from the mouse cursor to the nearest root endpoint.  Move the mouse cursor to the desired location for the new point.
    4. Press and release the left mouse button to set the point.



Moving a Diameter

Use the following steps to move a diameter:

    1. Select the root associated with the diameter to be moved.
    2. With the mouse cursor on the root's diameter, press and release the left mouse button.  Note: when the mouse's cursor is over the diameter, it is appear as a hand.
    3. Move the diameter along the root drawing until the desired diameter-drawing area has been reached.
    4. Press and release the left mouse button to drop the diameter at this point.



Resizing a Diameter

Use the following steps to move a diameter:

1.   Select the root associated with the diameter to be resized.

2.   With the mouse cursor on top-most portion of the root's diameter, press and release the left mouse button.  Note: when the mouse's cursor is over correct area,  it will appear as a two-sided arrow pointing north and south.

3.   Move the mouse cursor away from the root to increase the diameter length; move the cursor closer to the root to decrease its length.

4.   Press and release the left mouse button to set the diameter.



Moving Root Points

Individual points along a root can be moved.

Use the following steps to move a root point:

    1. Select the root associated with the point to be moved.
    2. With the mouse cursor on the desired root point, press and release the left mouse button.  Note: when the mouse's cursor is over a point, it appears as a icon with arrows pointing in the four cardinal directions.
    3. Move the point about the image window until the desired area has been reached.
    4. Press and release the left mouse button to drop the point.



Moving a Single Root


Use the following steps to move a single root:


    1. Select the root to be moved.
    2. With the mouse cursor on the desired root, press and release the left mouse button.  Note: The cursor cannot be over a point or the diameter.  An arrow cursor should be displayed when clicking on the root.
    3. Move the root about the image window until the desired area has been reached.
    4. Press and release the left mouse button to drop the root.



Moving All Roots

Use the following steps to move all roots:

    1. With the desired minirhizotron image in the image window, select the Move All Roots button , Edit > Move All Roots, or Ctrl + M.
    2. With the mouse cursor anywhere in the image window, press and release the left mouse button.
    3. The roots will not follow the movement of the mouse.  With the mouse, move the roots to the desired area.
    4. Press and release the left mouse button to drop the roots.



Deleting a Root

Use the following steps to delete a root:

    1. Select the root to be deleted.
    2. Select the Delete Root button , Edit > Delete Root, or Del keyboard key.
    3. A message "Delete Root #?" will appear.  Select "Yes" button.



Copying Roots Between Sessions


Before copying roots between sessions, make sure to know the session numbers being copied from and to and that they are correct.  Also note: any root information currently associated with a session will be deleted when another session is copied to it.  These roots cannot be recovered.


Use the following steps to copy roots between sessions:


    1. Select the Copy... option from the Edit menu, Edit > Copy..., or Ctrl + C.
    2. The dialog box below will appear (Image 1).  Select between: copying the roots in the current window # (the window displayed in the image window) of the current tube between sessions
    3. Input the session to copy roots from (in the first field) and the last session to receive the copied roots (the second field).  Example: having window 1 in the image window and "Current window of current tube" selected and "Copy from session 1 through session 5" in the below dialog will copy the root information in window 1 of session 1.  That information will be copied to window 1 of sessions 2, 3, 4, and 5.
    4. Select the "OK" button on the dialog.
    5. If necessary: If a window already has root data and it is receiving a copy of the root data from another session, a dialog box similar to Image 2 will appear.  If the copy should be made (and the data in the window overwritten), select "YES."


Image 1: Copy Session


Image 2: Confirm Overwrite


Viewing and Setting Root Properties


Being able to track root properties is perhaps the most important aspect of Rootfly for researchers.  To make this convenient for users to manipulate, the properties of a selected root can be viewed in the right pane.


This section of the pane (shown in the image at the right) both provides root properties and the opportunity for the user to set certain fields.


Root ID - This is the Root's ID within a given Window.  Root IDs are assigned to Root in the order that they are created, and they cannot be edited by the user.


Diameter - Based on the user calibration of Rootfly, the program will convert the selected root diameter's length in pixels to millimeters. 


Length - Based on the user calibration of Rootfly, the program will convert the selected root's length in pixels to millimeters. 


Color - The user can tell Rootfly the color of the selected root here.  The following color are available: white, light brown, dark brown, and black.


State - The user can tell Rootfly whether the root is alive or dead.


Custom - The user can give the selected Root a custom code.  By default, the only available code available within a project is "NO_CODE."  More codes can be added by coing to Edit > Custom Codes.



Image: Properties - Right Pane


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