McClean: Quickie ImageJ Quantification

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This is a quick and 'sloppy' way to segment cells and get an idea of their intensity. This is NOT really appropriate for carefully quantifying your data, but can at least give you an initial idea very quickly.



Instructions for "quickie" segmentation of cells and estimation of intensity data:

  1. Import your sequence of interest
    • File->Import->Image Sequence
    • In "Sequence Options" -> "or enter pattern" type "c1" (or c2, or c3, whichever wavelength you want, you can also use regular expressions in this box)
  2. Threshold the images
    • Image->Adjust->Threshold
    • Hit "Apply"
    • "Black Background" should be checked, hit "OK"
  3. Clean up the threshold image (the mask)
    • Process->Binary->Fill Holes (to fill in any holes in cells, ie vacuoles)
    • Process->Binary->Watershed (to break cells apart)
  4. Get "particles" (or cells in this case)
    • Analyze->Analyze Particles
    • Make sure "Add to Manager" is checked
    • Hit "OK"
  5. Repeat step 1
  6. Select all the ROI's in the ROI Manager
    • use shift, click the top ROI, then scroll to the bottom and click the last one
  7. Make sure measurements you want are checked
    • Analyze->Set Measurements
  8. Measure
    • Hit "Measure" in the ROI manager
  9. Save the Results manu that pops up after you clicked "Measure"
  10. Close all windows (including the ROI manager and results) and start again


Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input! Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.



or instead, discuss this protocol.