How to get the area of bare surface

[Steven Liu]

Hi,
Happy Valentine's Day!

I have an SEM image. There are network type particles on a substrate.
I want to calculate the area of bare substrate or particles.
I tried many ways to analyze it, but failed to get good segment.
Could anyone help me?
Thanks!

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[s c narula]

Dear Stevan LIU
You can try bone j plugin

Thanks

S c narula

On Thu 14 Feb, 2019, 10:22 AM Steven Liu, <[hidden email]> wrote:

> Hi,
> Happy Valentine's Day!
>
> I have an SEM image. There are network type particles on a substrate.
> I want to calculate the area of bare substrate or particles.
> I tried many ways to analyze it, but failed to get good segment.
> Could anyone help me?
> Thanks!
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Stein Rørvik]

This image cannot be thresholded the traditional way because of the shadowing effect from the substrate to the background. I have found the "Statistical Region Merging" to work great for many difficult segmentation problems. Try the below macro, and adjust the q and lower threshold value for best results.

run("Statistical Region Merging", "q=5 showaverages");
setThreshold(115.0000, 1e30);
run("Set Measurements...", "area mean area_fraction limit redirect=None decimal=9");
run("Measure");

The "Statistical Region Merging" plugin is included in the Fiji distribution; if you want to work in vanilla ImageJ 1.x you can just copy the plugin jar file from Fiji to ImageJ.

In the above macro, the bits of background touching the edge are not correctly segmented. You may try to expand the canvas with a similar greytone as the background to avoid these features being isolated.

"Statistical Region Merging" works even better with 3D stacks, but there is some overflow bug in it that causes it to fail with stacks above a certain size. You can work around this by splitting the stacks in smaller sections before processing. Since you are using SEM images they are 2D by nature so that will not be a problem for you.

Stein

-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Steven Liu
Sent: 14. februar 2019 04:28
To: [hidden email]
Subject: How to get the area of bare surface

Hi,
Happy Valentine's Day!

I have an SEM image. There are network type particles on a substrate.
I want to calculate the area of bare substrate or particles.
I tried many ways to analyze it, but failed to get good segment.
Could anyone help me?
Thanks!

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Kenneth Sloan-2]

"FindEdges" followed by Threshold looks promising
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.





> On Feb 14, 2019, at 05:21, Stein Rørvik <[hidden email]> wrote:
>
> This image cannot be thresholded the traditional way because of the shadowing effect  
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <MySnap 2019-02-14.png>

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[Steven Liu]

Dear Stein,
Thank you so much for your detailed introduction.
I followed your way.
It works well.
Thanks again.
Best regards,
Steven

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