Re: automated counting of triple labeled cells

Posted by Stoyan Pavlov on Aug 13, 2014; 6:37am
URL: http://imagej.273.s1.nabble.com/automated-counting-of-triple-labeled-cells-tp5009050p5009159.html

Image calculator is located in the Process menu.
Be careful because in Fiji there's also the Image calculator plus which is
NOT what you need for this . After the tool starts there are three
drop-down menus from which you choose the images for the arithmetic and the
operation to be executed (e.g. logical AND). There are additionally two
options - create new window and 32 bit, which are self explanatory. After
hitting OK the arithmetic operation is applied. The tool works on stacks as
well and can be recorded in a macro.
  Good tutorials for newcomers on the basic use of Fiji (Imagej) can be
found here :
http://imagej.nih.gov/ij/docs/examples/index.html
Good luck
Stoyan
 На 11.08.2014 00:40 "Liz Bless" <[hidden email]> написа:

> Thanks so much Stoyan! I don't know anything about the image calculator.
> Could you please direct me to where I can find it (and read up on it)?
>
> Thanks again!
> Liz
>
>
> On Fri, Aug 8, 2014 at 11:04 AM, Stoyan Pavlov <[hidden email]>
> wrote:
>
> > Hi Liz,
> > A simple solution is to binarize the three channels - red, green and
> > blue, which will produce black and white images of your cells. Using
> > analyze particles on the red channels you can count the red cells (1).
> > Then using logical AND-ing with the Image calculcator you can create
> > new images containing only the Red AND Blue (2), aswell as the Red AND
> > Blue AND Green (3) cells. And then again analyze with the Analyze
> > particles...
> >
> > Best wishes
> > Stoyan
> > ---
> > Dr. Stoyan P. Pavlov, MD, PhD
> > Departament of Anatomy, Histology and Embryology
> > Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> > Prof. Marin Drinov Str.55
> > 9002 Varna
> >  Bulgaria
> > Tel: +359 (0) 52 - 677 - 052
> > e-mail: [hidden email]
> >            [hidden email]
> >
> >
> > 2014-08-07 17:45 GMT+03:00 BioVoxxel <[hidden email]>:
> > > Hi Liz,
> > >
> > > If you can extract the labled cells as e.g. whiht particles on black
> > > background in a binary image, you can use the "Binary Feature
> Extractor"
> > > (see: http://fiji.sc/BioVoxxel_Toolbox#Binary_Feature_Extractor).
> > >
> > > You can either get this as part of the BioVoxxel Toolbox or if you want
> > to
> > > stick to ImageJ as a package to download from here:
> > > http://www.biovoxxel.de/macros.html
> > >
> > > Instructions are given on the respective site.
> > >
> > > This tool only always compares 2 images with each other but you can do
> > your
> > > analysis easily in separate steps and thereby get an idea of all
> possible
> > > combination of double positive stainings as well as even triple
> positive
> > > ones. The latter can be achieved if you run the analysis with one of
> your
> > > original images and one output image from a previous analysis using the
> > > very same tool.
> > >
> > > Let me know if you need further help.
> > >
> > > regards,
> > > Jan
> > >
> > >
> > > 2014-08-06 22:21 GMT+02:00 Liz Bless <[hidden email]>:
> > >
> > >> Hi -
> > >>
> > >> I have IHC images that contain 3 labels. I would like imageJ to be
> able
> > to
> > >> automatically count 1) the number of red cells in the image, 2) the
> > number
> > >> of red cells that are also blue, 3) the number of red cells that are
> > also
> > >> blue and green.
> > >>
> > >> I know how to count single labeled cells but could anyone direct me
> to a
> > >> plugin for counting double and triple labelled cells or advise me on
> > how to
> > >> go about this?
> > >>
> > >> Thank you!
> > >> Liz
> > >>
> > >> --
> > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >>
> > >
> > >
> > >
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