automated counting of triple labeled cells

[Liz Bless]

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

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[gankaku]

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
>

--

CEO: Dr. rer. nat. Jan Brocher
phone:  [phone]
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[Stoyan Pavlov]

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
>>
>
>
>
> --
>
> CEO: Dr. rer. nat. Jan Brocher
> phone:  [phone]
> mobile: [phone]
> e-mail: [hidden email]
> info: [hidden email]
> inquiries: [hidden email]
> web: www.biovoxxel.de
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Liz Bless]

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
> >>
> >
> >
> >
> > --
> >
> > CEO: Dr. rer. nat. Jan Brocher
> > phone:  [phone]
> > mobile: [phone]
> > e-mail: [hidden email]
> > info: [hidden email]
> > inquiries: [hidden email]
> > web: www.biovoxxel.de
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stoyan Pavlov]

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
> > >>
> > >
> > >
> > >
> > > --
> > >
> > > CEO: Dr. rer. nat. Jan Brocher
> > > phone:  [phone]
> > > mobile: [phone]
> > > e-mail: [hidden email]
> > > info: [hidden email]
> > > inquiries: [hidden email]
> > > web: www.biovoxxel.de
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html