We have a similar problem and we solve it experimentally thus:
We are interested in the immunocytochemical staining of nuclear proteins
with a fluorophore attached to the antibody of interest.
To find the nuclear outline, we stain all slides also with DAPI which
specifically stains only DNA.
Then we examine the slides with the DAPI filters and take a photograph
and then photograph the same field with the fluorophore filter.
The photos are then examined and read with a macro especially written
for this purpose for ImageJ, by Dr Pawel Znojek when he was at the
University of Newcastle in Northern England.
He has told me that he has uploaded this macro, but I obtained a copy
from his website which is at;
http://www.PZfociEZ.com/index.htmlIf you decide to try this macro, I would be very interested to hear how
you get on.
With best wishes,
Sydney
On 27/12/2011 21:30, Benjamin Grant wrote:
> Hi All,
> I'm working on the automated analysis of some cellular images that our lab
> takes. We simply calculate the nuclear to cytoplasm ratio in our images. I
> have no problem in automatically finding the nuclei in the images once the
> user has selected an ROI based on which region is subjectively the
> clearest. I'd definitely like to remove the user input for the ROI but am
> struggling to find a way to automatically do it. I don't know what features
> to use to select an ROI that is "clearer" and has less background. I
> provided a raw image here:
http://i.imgur.com/yVcoz.jpg and the same image
> with an experienced user's ROI selection and automated nuclei detection:
>
http://i.imgur.com/Aaokk.png. Another example is raw here:
>
http://i.imgur.com/ywqiU.jpg and ROI + nuclei here:
>
http://i.imgur.com/3h9Ta.png Does anyone have any general suggestions on
> automating this process? thanks in advance
> Ben
--
Professor Sydney Shall,
Department of Haematological Medicine,
King's College London,
Medical School,
123 Coldharbour Lane,
LONDON SE5 9NU,
Tel& Fax: +44 (0)207 848 5902,
E-Mail: sydney.shall,
[correspondents outside the College should add; @kcl.ac.uk]
www.kcl.ac.uk
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