Analyzing a grid of cells

Hi All,

I am interested in some imaging processing and analysis of data I have been collecting. I would like to get some statistics on the intensity of the cells in this grid.

Some processing steps would include:
-straighten and crop the array found in the center of the images below.
-apply a grid with a predefined number of rows and columns over the image such that each cell is indexed to the grid
-analyze each cell location and get statistics about brightness (the majority of cells are not emitting)
-determine the population of cells that are emitting

Apply this process over a set of images.

I am agnostic as to which software to use to do this. Please let me know your thoughts on how to get started with this.

Thanks

Hello
Does this can help you out with wath you want ?

run("Rotate… ", “angle=-4 grid=1 interpolation=None”);
//setTool(“rotrect”);
makeRotatedRectangle(1590, 1104, 3342, 1104, 676);
run(“Crop”);
run(“Select None”);
run(“32-bit”);
run(“Bandpass Filter…”, “filter_large=40 filter_small=3 suppress=None tolerance=5”);
setAutoThreshold(“RenyiEntropy dark”);
//run(“Threshold…”);
run(“Convert to Mask”);
run(“Erode”);
run(“Erode”);
run(“Watershed”);
run(“Analyze Particles…”, “display add”);
roiManager(“Show All without labels”);
roiManager(“Show All with labels”);

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Thank you for the suggestion, is what you wrote a macro for imagej?

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