McClean: Quickie ImageJ Quantification: Difference between revisions

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(New page: 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...)
 
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<!-- COPY EVERYHING BELOW HERE TO START YOUR OWN PROTOCOL!  -->


==Overview==
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.






==Materials==
* [http://fiji.sc/wiki/index.php/Fiji FIJI ImageJ ]
* Images






==Protocol==




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


1. Import your sequence of interest
# Import your sequence of interest
File->Import->Image Sequence
#*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)
#*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
# Threshold the images
Image->Adjust->Threshold
#*Image->Adjust->Threshold
Hit "Apply"
#*Hit "Apply"
"Black Background" should be checked, hit "OK"
#*"Black Background" should be checked, hit "OK"
3. Clean up the threshold image (the mask)
# Clean up the threshold image (the mask)
Process->Binary->Fill Holes (to fill in any holes in cells, ie vacuoles)
#*Process->Binary->Fill Holes (to fill in any holes in cells, ie vacuoles)
Process->Binary->Watershed (to break cells apart)
#*Process->Binary->Watershed (to break cells apart)
# Get "particles" (or cells in this case)
#*Analyze->Analyze Particles
#*Make sure "Add to Manager" is checked
#*Hit "OK"
# Repeat step 1
# 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
# Make sure measurements you want are checked
#*Analyze->Set Measurements
# Measure
#*Hit "Measure" in the ROI manager
# Save the Results manu that pops up after you clicked "Measure"
# Close all windows (including the ROI manager and results) and start again


4. Get "particles" (or cells in this case)
==Notes==
Analyze->Analyze Particles
<!-- Please paste this section "as is" into your protocol, and add notes to it if you have some!-->
Make sure "Add to Manager" is checked
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 <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip.
Hit "OK"


5. Repeat step 1
==References==


6. Select all the ROI's in the ROI Manager
==Contact==
use shift, click the top ROI, then scroll to the bottom and click the last one
<!--Change the information below to your info if you add a new protocol-->
*'''[[User:Megan N McClean|Megan N McClean]] 14:01, 20 July 2011 (EDT)'''


7. Make sure measurements you want are checked
or instead, [[Talk:{{PAGENAME}}|discuss this protocol]].  
Analyze->Set Measurements


8. Measure
<!-- You can tag this protocol with various categories. See the [[Categories]] page for more information. -->
Hit "Measure" in the ROI manager
[[Category:Protocol]]


9. Save the Results manu that pops up after you clicked "Measure"
<!-- Move the relevant categories above this line to tag your protocol with the label
[[Category:Protocol]]


10.  Close all windows (including the ROI manager and results) and start again
-->

Latest revision as of 14:19, 23 January 2012


Overview

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.


Materials


Protocol

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

Notes

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.

References

Contact

or instead, discuss this protocol.


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