Re: percentage of area covered by cells

Posted by gankaku on Nov 28, 2014; 11:20am
URL: http://imagej.273.s1.nabble.com/percentage-of-area-covered-by-cells-tp5010672p5010674.html

Hi Diana,

Could you attatch also a example image after your extraction procedure
(binary image after the thresholding)?
Then it might be easier to find the problem or explanation.
When I try to repeat your described method with a quick extraction (while
my thresholding will obviously be different from yours), I end up with
values between 35 or 45% (Area fraction) depending upon the threholding I
apply. But it seems those are realistic values in comparison to what I see
in my image.
A potential problem might be that you background option is not set
correctly. This you can check under >Process >Binary >Options... to figure
out if ImageJ considers the background to be black or white. In conjunction
with this, your output image might be displayed with an inverted LUT (for
whatever reason) which would give you in inverted measurement in comparison
to what you would consider as being foreground (features of interest).
Additionally make sure that you do not have any selection present in the
image. Otherwhise, the area fraction is determined only from within your
ROI.

Hope this helps already. With a binary image posted we might help you
further.
Kind regards,
Jan

2014-11-28 11:49 GMT+01:00 dianalves <[hidden email]>:

> Hi everyone,
>
> I am a new user of ImageJ and I would be very grateful for any help with
> the
> following problem.
> I want to use ImageJ to calculate total percentage of area covered by
> bacteria and distinguish the fraction of dead and live cells. For that I am
> using a live or dead staining where live cells are stained in green and
> dead
> cells in red. I obtained a single grayscale image for each fluorescence
> channel and after subtracting background, I set a thereshold value manually
> for each image.  Afterwards I went to Measure and checked Area and Area
> fraction (%). I thought that the values of Area fraction was the percentage
> of area covered but the values seem to low. For instance, the percentage of
> area covered for the image I have attached (if I consider area fraction) is
> of about 10%. Can you please let me know if I am doing something wrong or
> not interpreting the values as I should?
> Thanks in advance for any ideas!
> <http://imagej.1557.x6.nabble.com/file/n5010672/Live_cells.png>
>
>
>
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>
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