McClean: Quickie ImageJ Quantification

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