The Nanoscale World

Particle Analysis using Nanoscope Analysis

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JSUO posted on Wed, Oct 24 2012 3:48 PM

Dear friends,

I am a bit confused on the definition of the “threshold height” used in the particel analysis function of the image analysis software (Nanoscope Analysis, v1.4). I found that the average particle height given in the statistics sometimes is less the threshold height I input. My understanding of the threshold height is defined relative to the image mean (the substrate), but this may be incorrect. Although one can always do the particle analysis by looking at the highlighted particles in the image and use the number for threshold height as a relative value, it would be nice to understand how it is defined precisely.

Also the help files do not explain well the meaning of the "Non-Representative Particles". Many particles can be included or excluded by enable / disable this option. Anyone can help to clarify this?

Thank you for help.

Jahson

 

 

 

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Suggested by Vinson Kelley

JSUO:

Dear friends,

I am a bit confused on the definition of the “threshold height” used in the particel analysis function of the image analysis software (Nanoscope Analysis, v1.4). I found that the average particle height given in the statistics sometimes is less the threshold height I input. My understanding of the threshold height is defined relative to the image mean (the substrate), but this may be incorrect. Although one can always do the particle analysis by looking at the highlighted particles in the image and use the number for threshold height as a relative value, it would be nice to understand how it is defined precisely.

Also the help files do not explain well the meaning of the "Non-Representative Particles". Many particles can be included or excluded by enable / disable this option. Anyone can help to clarify this?

Thank you for help.

Jahson

 

Hi Jahson.


The user defines Threshold Height. Output heights (e.g. Average Height...) displayed in the Detect Tab Data Box are computed relative to this Threshold Height.

I personally find X Axis (Relative) confusing. It is relative to the highest, not lowest, peak. I prefer Absolute, but that's just me.

Setting Non-Representative Particles to No filters out particles whose area is less than the average area minus 3 sigma of that area. Setting Non-Representative Particles to Yes includes everything above the Threshold Height. You may also wish to set Boundary Particles to Yes to include partial particles.

Regards,

Vinson Kelley

 

 

 

 

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JSUO replied on Mon, Oct 29 2012 2:01 PM

Hi, Vinson,

Thank you for your kind reply.

I agree that the thredshold shlould be input by the user and the output height is generated by the software. I think what is missed in my understanding is the physical definition of this "threshold", since the output statistics varies significantly when this threshould changes. When comparing the particle analysis results for multiple images, it is critical to run the particle counting with identical criteria. For example, all the small particles with height less than 0.5nm are ignored. I assume this 0.5 nm is what the threshold means and tried to maintain the same thresold for the same group of images, but got confused when I saw the output showing, sometimes, partilces lower than 0.5 nm. If the threshold means the exclusion of any particles higher / lower, then why do I still see particles in the output statistics that should have been excluded? I guess my question is more like how does the software use this threshlod to determine and measure a particle? Thanks again.

Best,

Jahson

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Hi Jahson,

I suggest that you set Height Reference to Relative to Threshold for more repeatable results.

Regards,

Vinson Kelley

 

 

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