Muscle fiber analysis

Hi everyone,
i have a mouse muscle section stained with succinate. With these staining i can see three muscle fiber types (dark, middle-dark and white). I would like to count and to outline them. But i had some problems. When i try so separate the fibers with the watershed the program counts some fibers as one and some fibers he splits into many pieces. Maybe someone can help me or has an idea what i can optimize or change…

Thank you!
Diana2 10x TA sdh - Copy.tif (4.0 MB)

2 10x TA sdh - Copy.tif (4.0 MB)

Hi
@Diana

Far from perfect …but a work track.

requires("1.52u");
setBackgroundColor(0,0,0);
setOption("BlackBackground",true);
img=getImageID();
selectImage(img);
//setTool("rectangle");
makeRectangle(0, 0, 1360, 990);
run("Crop");
run("Duplicate...", "title=1");
close("\\Others");
run("Duplicate...", "title=2");
run("32-bit");
run("Scale...", "x=0.4 y=0.4 width=544 height=410 interpolation=Bilinear average create");
morpholib();
run("Scale...", "x=2.5 y=2.5 width=1360 height=1025 interpolation=Bilinear average create");
setAutoThreshold("IJ_IsoData dark");
//run("Threshold...");
//setThreshold(151, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
run("Analyze Particles...", "display exclude include add");
selectWindow("1");
setBatchMode(false);
roiManager("Show All without labels");
exit("Completed");

function morpholib()
{
run("Morphological Segmentation");
selectWindow("Morphological Segmentation");
//setTool("point");
wait(2000);
call("inra.ijpb.plugins.MorphologicalSegmentation.setInputImageType", "object");
call("inra.ijpb.plugins.MorphologicalSegmentation.setGradientRadius", "1");
call("inra.ijpb.plugins.MorphologicalSegmentation.setGradientType", "Morphological");
wait(1000);
call("inra.ijpb.plugins.MorphologicalSegmentation.setDisplayFormat", "Watershed lines");
call("inra.ijpb.plugins.MorphologicalSegmentation.segment", "tolerance=10.0", "calculateDams=true", "connectivity=4");
wait(2000);
call("inra.ijpb.plugins.MorphologicalSegmentation.createResultImage");
wait(1000);
selectWindow("Morphological Segmentation");
close();
print("\\Clear");
}