Clumping Area Imaging

I am trying to measure the area occupied by cell clumping. When they didn’t clump I had a macro which worked which was able to distinguish the cells. Now since there is so many it seems impossible and I just want to see how much area is taken up. I attempted to merge the close objects and count the area, but there is still many gaps where the cells are not being counted as area taken up. Any recommendations on how I could fill in this area or ways to quantify this? Attached is the macro i’m using and an example image. The images in color show the project and the merging of objects but still a lot of area that is not counted. 48hrcontrol_outlet002.tif (8.8 MB) 48hr0.1ug_outlet.tif (9.3 MB) Thanks,Area_count.cpproj (1022.3 KB)

Hi @Sps


Using Image J
Can such a result be suitable?
Let me know
Thank you
Agglomération de cellules.tif (12.0 MB)Preformatted text

Here is the macro I used.


run("Duplicate...", "title=1");
run("Duplicate...", "title=2");
run("32-bit");
run("Morphological Segmentation");
selectWindow("Morphological Segmentation");
//setTool("multipoint");
wait(1000);
call("inra.ijpb.plugins.MorphologicalSegmentation.setInputImageType", "object");
call("inra.ijpb.plugins.MorphologicalSegmentation.setGradientRadius", "1");
call("inra.ijpb.plugins.MorphologicalSegmentation.setGradientType", "Morphological");
call("inra.ijpb.plugins.MorphologicalSegmentation.segment", "tolerance=23.0", "calculateDams=true", "connectivity=4");
call("inra.ijpb.plugins.MorphologicalSegmentation.setDisplayFormat", "Catchment basins");
wait(10000);
call("inra.ijpb.plugins.MorphologicalSegmentation.createResultImage");
wait(10000);

selectWindow("2-catchment-basins");
run("RGB Color");
run("RGB to CMYK");
selectWindow("CMYK_2-catchment-basins");
run("Stack to Images");
selectWindow("Y");
run("Gaussian Blur...", "sigma=10");
run("Select None");
//setTool("wand");
doWand(15, 1125, 0.12, "Legacy");
selectWindow("Y");
roiManager("Add");
roiManager("Select", 0);

selectWindow("1");
roiManager("Select", 0);
roiManager("Show All");
roiManager("Select", 0);
setBackgroundColor(0, 0, 0);
run("Clear", "slice");
run("Select None");
roiManager("Show None");