Posted by
Romain Guiet on
Jan 07, 2015; 8:29am
URL: http://imagej.273.s1.nabble.com/Multinucleate-automatic-cell-counting-tp5011083p5011108.html
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/---------------------------------------------------------------
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De : ImageJ Interest Group [
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Envoyé : lundi 5 janvier 2015 22:28
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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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