LeBauer:Protocol/rootlength

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Overview

Replace this sentence with a brief description of the protocol and its goal.

Converting Root Images to Binary

Software

ImageJ=NIHimage=SCIONimage or Gimp

(both free, Gimp may have more tools for this step, it is like Adobe Photoshop)

Image Binarization

Practice converting images from color to binary

this is just practice to get used to the task Goal: turn roots black and background white Tools: brightness, contrast, pen, brush, eraser, whatever else is necessary

1. Create four replicates from each of two images
   1. Open the first image imagename.tiff
   2. crop the image to exclude below the black line
   3. cut remaining area of image into four quarters
   4. save each quarter as a separate file as imagename1.tiff imagename2.tiff... ""3.tiff ""4.tiff
2. Practice binarazation
   1. Take 20 min to convert imagename1.tiff to binary and save as imagename1_20min.tiff
   2. repeat, taking 10 min
   3. repeat, taking 5 min.
   4. repeat 3.1-3.3 for each of four parts of original image
   5. open next image and return to 1.1.
3. Determine the ratio of black to white in each of the above images
   1. Fill in step-by-step details here
4. Check relative strength of each source of error: time spent converting, within image variability, and between images
   1. make a table of time x sample number (8 total samples, three times)
   2. compare σ²_subsamples, σ²_time, σ²_image.

Materials

List reagents, supplies and equipment necessary to perform the protocol here. For those materials which have their own OWW pages, link to that page. Alternatively, links to the suppliers' page on that material are also appropriate.

• supply 1 (i.e. tubes of a certain size? spreaders?)
• reagent 1
• X μL reagent 2
  • component A (reagent 2 is made up of multiple components)
  • component B
• equipment 1
• equipment 2

Procedure

1. Step 1
2. Step 2
   • Step 2 has some additional information that goes with it. i.e. Keep at 4°C.
3. Step 3
   1. Step 3 has multiple sub-steps within it.
   2. Enumerate each of those.

Notes

Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

1. List troubleshooting tips here.
2. You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
3. Anecdotal observations that might be of use to others can also be posted here.

Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.

References

Relevant papers and books

1. Methods for studying roots [Bohm]
2. ISBN:354009329X

   [bohm1979msr]

Contact

• Who has experience with this protocol?

David LeBauer

or instead, discuss this protocol.