Multinucleate automatic cell counting?

[Monkey]

I am trying to automate image analysis for high-throughput scoring of cells,
where I would like to extract the percentage of multinucleate versus
mononucleate cells.  I have used the BioVoxxel plugin to select cell bodies
(as objects) from one binary image layer using a DAPI nuclear stain binary
image layer (as selector) to weed out dead cells.

This worked well, but now I want extract information about multinuclearity:

    1)  How many nuclei (from binary DAPI image) overlap with the cell body
(from binary cell body image, TRITC channel, labeling cells of interest in
contrast to other cells in a co-culture)

    2)  For each overlapping nucleus, does it lie on the border of the cell
body (since these may not be a part of the cell of interest, and I will have
to either manually check them or work out an automated method to exclude the
possibility they are from a different type of cell than the one I am
interested in)?

I imagine it would not be too difficult to code, but I was wondering if
anyone knows of a plugin that can already do this?

Many thanks for any help!

Justin



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[Robert Baer]

You might take a look at cell profiler for this type of high throughput
task: http://www.cellprofiler.org/

Rob
On 1/5/2015 3:28 PM, Monkey wrote:

> I am trying to automate image analysis for high-throughput scoring of cells,
> where I would like to extract the percentage of multinucleate versus
> mononucleate cells.  I have used the BioVoxxel plugin to select cell bodies
> (as objects) from one binary image layer using a DAPI nuclear stain binary
> image layer (as selector) to weed out dead cells.
>
> This worked well, but now I want extract information about multinuclearity:
>
>      1)  How many nuclei (from binary DAPI image) overlap with the cell body
> (from binary cell body image, TRITC channel, labeling cells of interest in
> contrast to other cells in a co-culture)
>
>      2)  For each overlapping nucleus, does it lie on the border of the cell
> body (since these may not be a part of the cell of interest, and I will have
> to either manually check them or work out an automated method to exclude the
> possibility they are from a different type of cell than the one I am
> interested in)?
>
> I imagine it would not be too difficult to code, but I was wondering if
> anyone knows of a plugin that can already do this?
>
> Many thanks for any help!
>
> Justin
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Multinucleate-automatic-cell-counting-tp5011082.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Monkey]

This software looks amazing!  Thanks for the reply Rob!

-justin

[Romain Guiet]

Hi Justin,


Using Image/Fiji and the recorder and you can easily :
For the 1st part :
1- create some region of interest (ROI) for the nuclei using run("Analyze Particles...");
2- Using a loop you get the centerOfMassCoordinatesOfNuclei from the results table using the function getResults(Column,row,index) and store them in some arrays with a loop.
3- create ROIs for the cell bodies using run("Analyze Particles...");
4- Using a loop (again) and functions like roiManager(“Select”, index) and Roi.contains(x, y), you can count how many nuclei per cell body...

For the 2nd part :
On your segmented image of the cell bodies you could try to use run("Geometry to Distance Map", …); to generate a distance map image and Using the centerOfMassCoordinatesOfNuclei and a cut-off value decide if they are too close of the border…

Hope it could help,

Romain

---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne

Phone: [+4121 69] 39629
http://biop.epfl.ch/
---------------------------------------------------------------

________________________________________
De : ImageJ Interest Group [[hidden email]] de la part de Monkey [[hidden email]]
Envoyé : lundi 5 janvier 2015 22:28
À : [hidden email]
Objet : Multinucleate automatic cell counting?

I am trying to automate image analysis for high-throughput scoring of cells,
where I would like to extract the percentage of multinucleate versus
mononucleate cells.  I have used the BioVoxxel plugin to select cell bodies
(as objects) from one binary image layer using a DAPI nuclear stain binary
image layer (as selector) to weed out dead cells.

This worked well, but now I want extract information about multinuclearity:

    1)  How many nuclei (from binary DAPI image) overlap with the cell body
(from binary cell body image, TRITC channel, labeling cells of interest in
contrast to other cells in a co-culture)

    2)  For each overlapping nucleus, does it lie on the border of the cell
body (since these may not be a part of the cell of interest, and I will have
to either manually check them or work out an automated method to exclude the
possibility they are from a different type of cell than the one I am
interested in)?

I imagine it would not be too difficult to code, but I was wondering if
anyone knows of a plugin that can already do this?

Many thanks for any help!

Justin



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