Imaging

Link: https://ij.imjoy.io/

How to measure your bacteria

1. File > Open > find your picture
   
2. Draw a line across the diameter of your petri dish
3. Set the scale of your picture
   1. Analyze > Set Scale
   2. Change known distance to 100
   3. Change Unit of length to mm
   4. Hit Ok
4. Image > Adjust > Color Threshold
   1. Adjust the two top dials until all of your bacteria are red but not most of the other things in the picture
   2. Change the Thresholding method if necessary as well
   3. When you are happy, close the image
5. FROM HERE--Two choices
   1. Manually select each colony with the magic wand or circle tool in the toolbar
      1. Click on the Magic Wand tool in the toolbar
      2. Hold down shift and manually click on your bacteria colonies
   2. Process > Binary > Convert to Mask
6. Analyze > Analyze Particles
   1. If needed, adjust the maximum size to eliminate any large blobs (like fingers)
   2. Change Show: to "Overlay"
   3. Check "Display Results" 
   4. Check "Summarize"
   5. Click OK
7. Look at your summary and results, check if all your colony numbers make sense and that your area total makes sense. If not, check your calibration or adjust which particles you added
8. Record your results