imageJ: Cell Overlap with Multiple Filters

Image Analysis
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#1

Hi all,

I’m trying to use ImageJ’s analyze particles tool to count cells in images with cells and background tissue stained in different colors (red, magenta, green, and blue).

I have got the program to count cells for each image, one at a time. However, since I’m working with different filters/colors, I have to account for overlapping cells so that cells are not counted twice. I was wondering if there is an existing tool that detects and outputs overlapping cells or if there is a feature that outputs the x and y coordinates of the counted cells. With the coordinate values, I could write a program that outputs which cells were counted more than once with the different filters.

If not, are there alternative programs that I can use other than ImageJ? Thank you in advance for your help!

#2

Have a look at the ROIManager and ROI macro API of ImageJ:

Overlapping cells could be detected, e.g. with:

Roi.contains(x, y)
https://imagej.nih.gov/ij/developer/macro/functions.html#Roi.contains

Roi.getContainedPoints(xpoints, ypoints)
https://imagej.nih.gov/ij/developer/macro/functions.html#Roi.getContainedPoints

So you could for example add your cell selections to the ROI Manager (for each color) and then write a script to iterate over the ROI’s in the ROI Manager and detect overlapping cells.

See also:
https://imagej.nih.gov/ij/macros/ROI_Manager_Stack_Demo.txt

Another vague idea (only for counting) would be to simply apply a boolean ‘And’ operation to all ROI’s and count a created result (cells with overlap).

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