Issues processing images

imagej
segmentation

#1

Hi there,

I have some issues with the processing of some images. I have like 100/200/500/1000 or more pictures per condition (temperature), and I have several for different materials hence I have a lot. I observe crystallization, so I decide to analyze an individual crystal instead of the collection that I have on the full picture. I would like to get the particle size evolution for each condition and much parameters as I can.

I process the images with the following options. The main problem is using Threshold.

run(“Gaussian Blur…”, “sigma=2”);
run(“Median…”, “radius=2”);
run(“Find Edges”);
run(“Enhance Contrast…”, “saturated=3 normalize”);

run(“Threshold…”);

run(“Convert to Mask”);
run(“EDM Binary Operations”, “iterations=1 operation=dilate”);
run(“EDM Binary Operations”, “iterations=2 operation=close”);
run(“Fill Holes”);
run(“EDM Binary Operations”, “iterations=3 operation=open”);
run(“EDM Binary Operations”, “iterations=3 operation=erode”);

run(“Analyze Particles…”, “size=10-Infinity display exclude clear summarize add in_situ”);

However, it works just for one image and not for the remaining, also I have tried other options like e.g substrate background, weka segmentation or morphological segmentation, any suggestion is welcome!

Regards.

Ed

For some reason, I can not upload my images. Take a look at the link please: https://drive.google.com/drive/folders/1o1hM1V08KbmbzIkffkEpMRtWu_gOSdxg?usp=sharing


#2

The Threshold problem can be resolved by replacing it
run(“Threshold…”);
with
setAutoThreshold(“Default dark”);
//run(“Threshold…”);
//setThreshold(87, 255);
setOption(“BlackBackground”, true);
Macro should look like this:
run(“Gaussian Blur…”, “sigma=2”);
run(“Median…”, “radius=2”);
run(“Find Edges”);
run(“Enhance Contrast…”, “saturated=3 normalize”);
setAutoThreshold(“Default dark”);
//run(“Threshold…”);
//setThreshold(87, 255);
setOption(“BlackBackground”, true);
run(“Convert to Mask”);
run(“EDM Binary Operations”, “iterations=1 operation=dilate”);
run(“EDM Binary Operations”, “iterations=2 operation=close”);
run(“Fill Holes”);
run(“EDM Binary Operations”, “iterations=3 operation=open”);
run(“EDM Binary Operations”, “iterations=3 operation=erode”);
run(“Analyze Particles…”, “size=10-Infinity display exclude clear summarize add in_situ”);

Best regards,
Ion (Naikos).


#3

Hi @andronacheion,

Thanks for your response, I think still it is not working. Just works for some images but for all. Take a look at my images.
https://drive.google.com/drive/folders/1o1hM1V08KbmbzIkffkEpMRtWu_gOSdxg?usp=sharing.

Cheers.

Ed


#4

You should probably normalize the intensities of your images before applying the threshold. Have a look at this post.