[Gwyddion-users] Particles/Grains shape

[Judy Phan]

Hi,
I'm working on a project where particles are collected and imaged using the
AFM. I've been getting myself familiar with Gwyddion software. My goal is
to be able to quantify the particles using the grain properties tools but
since I'm working with multiple particles, I need to normalized their
properties in order to compare them. So far, I saw people done 2-D
parameters such as elongation, convexity, circularity, etc. Does anyone
know what are the 3-D parameters? I think comparing the ratios of the major
and minor semiaxis of equivalent ellipse with the mean height will give me
some sort of elongation. For convexity (surface roughness), in 2-D it is a
ratio between the particle area and the total area. Is projected area the
total area? And is the surface area actually the particle area? I'd like to
translate this to 3-D ratio.

Thanks,

[luis vazquez]

Dear Judy,

I do not know about the parameters you are asking about, however, I just
wanted to note you that you should be aware of tip convolution effects
in AFM measurements. I do not know the size of your particles and the
tip dimensions but, in principle, the height of the particle would be a
more reliable measurement than its lateral dimensions as in the later
the tip convolution effects will be more marked.

Regards,
Luis

Post by Judy Phan
Hi,
I'm working on a project where particles are collected and imaged
using the AFM. I've been getting myself familiar with Gwyddion
software. My goal is to be able to quantify the particles using the
grain properties tools but since I'm working with multiple particles,
I need to normalized their properties in order to compare them. So
far, I saw people done 2-D parameters such as elongation, convexity,
circularity, etc. Does anyone know what are the 3-D parameters? I
think comparing the ratios of the major and minor semiaxis of
equivalent ellipse with the mean height will give me some sort of
elongation. For convexity (surface roughness), in 2-D it is a ratio
between the particle area and the total area. Is projected area the
total area? And is the surface area actually the particle area? I'd
like to translate this to 3-D ratio.
Thanks,
--
Judy Phan
Master of Science in Chemical Engineering, 2015
Bachelor of Science in Chemical Engineering with Cum Laude, 2013
Bucknell Engineering Network Student Liaison
Chair of the Banquet & Society Activities Committee of Tau Beta Pi
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[David Nečas (Yeti)]

Post by Judy Phan
For convexity (surface roughness), in 2-D it is a
ratio between the particle area and the total area. Is projected area the
total area? And is the surface area actually the particle area?

Projected area is the area of the particle projection onto the xy plane.
Surface area is the surface area. It is estimated by triangulation[1]
and it is always greater than or equal to the projected area. Of
course, AFM only sees the upper surface (and even then with tip
convolution).

Regards,

Yeti


[1] http://gwyddion.net/documentation/user-guide-en/statistical-analysis.html#surface-area-calculation

[Mark S. Bentley]

Dear all,

I'm looking for a way to set all data windows to display "physically
square" rather than "pixelwise square". Either by setting this in the
GWY files when I generate them, or via a pygwy script for open files.

I couldn't see anything obvious in either the file description or
gwy.DataWindow docs. Is this possible?

Many thanks,

Mark

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[David Nečas (Yeti)]

Post by Mark S. Bentley
I'm looking for a way to set all data windows to display "physically
square" rather than "pixelwise square". Either by setting this in the
GWY files when I generate them,

Store TRUE to

/N/data/realsquare

where N is the channel number for all channels.

Post by Mark S. Bentley
or via a pygwy script for open files.

Via pygwy you can do the same, but if you are generating GWY files you
can directly create them as you want

Regards,

Yeti


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[Mark S. Bentley]

Perfect! I don't know how I missed that in the file format description :-s

Many thanks!

Mark

Post by David Nečas (Yeti)

Post by Mark S. Bentley
I'm looking for a way to set all data windows to display "physically
square" rather than "pixelwise square". Either by setting this in the
GWY files when I generate them,

Store TRUE to
/N/data/realsquare
where N is the channel number for all channels.

Post by Mark S. Bentley
or via a pygwy script for open files.

Via pygwy you can do the same, but if you are generating GWY files you
can directly create them as you want
Regards,
Yeti

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