TITLE: RootBot Image Scoring Instructions
AUTHORS: Mia Ruppel, Sven K. Nelson, Grace Sidberry, Madison Mitchell, Daniel Kick, Shawn K. Thomas, Katherine E. Guill, Melvin J. Oliver, Jacob D. Washburn

[DESCRIPTION]
Instruction for scoring RootBot images.

[STEPS]
SECTION: Installation and setup
1. Download and install Image J (https://imagej.net/software/fiji/downloads) 
SECTION: Installation and setup
2. Download the Smart Root Explorer plugin by following the website instructions
a) Website - https://smartroot.github.io/SmartRoot-Installation/
b) Instructions - on the SR Explorer website click SmartRoot quickstart under downloads
2. 
SECTION: Process root images
3. Open Image J and go to the plugins tab in the upper left hand corner and click SR Explorer.  

SECTION: Process root images
4. Once the SR Explorer plugin is active go to the SmartRoot window and click on the Settings tab.
SECTION: Process root images
4.1. Under Image resolution select pixels/cm and change the values to 330 pixels/1cm -> click apply.
SECTION: Process root images
4.2. Under Naming options change the Principal root prefix to “name of your seed”seed#  -> click apply.
  
SECTION: Process root images
5. Move to the SmartRoot Explorer window and select your .jpg image (a “wrong image type…” warning will appear -> click okay).
SECTION: Process root images
5.1. Copy the name of your file.
SECTION: Process root images
5.2. Save the image as a .tiff into the "Already Scored" folder. This is simply a folder used to keep the scored images organized. If it does not exist, create it.
SECTION: Process root images
5.3. The image will appear in greyscale. You can increase display brightness on your computer for greater contrast between roots and soil.
SECTION: Process root images
6. Click on the magnifying glass icon in the (Fiji is Just) ImageJ window.  With the magnifying glass selected, click the center of the image once to zoom in.
SECTION: Process root images
7. Click on the Trace Root icon in the (Fiji is Just) ImageJ window.
 
SECTION: Process root images
8. While holding down the shift key, left-click on the top of the root and trace downwards using clicks to fix the tracing line to the root (Double-click to end the tracing).
SECTION: Save the output data
11. To save the data go to the SmartRoot Window and click on the Data transfer tab.
SECTION: Save the output data
11.1. Unselect Send to SQL database.
SECTION: Save the output data
11.2. Select Send to CSV. Click "Choose" and paste the name of your original image as the name.  Then save to the "Already Scored" folder as a comma-separated value -> then hit save.
SECTION: Save the output data
11.3. Select Send tracing to image file. Under image type select Black and White and png. Click "Choose" and paste the name of your original image as the name. Then save to the "Already Scored" folder -> then click save.
SECTION: Save the output data
11.4. Click Transfer tracing data.
  
SECTION: Save the output data
12. Go to your "Already Scored" folder and open the .csv file, check to make sure that all 10 roots are properly named and scoring data is present.
SECTION: Save the output data
13. Close the .tif image and ensure that it appears in the Already Scored Folder. There should be four files in the folder: .csv, .png, .rsml, and .tif.
None. 
SECTION: Process root images
9. Repeat steps 8 and 9 for all roots.
SECTION: Process root images
10. An input window will appear with “name”seed#0 change the 0 to the corresponding seed number in the plate (1-10) ->  then click okay.