Thickness plugin 3D mapping

[ayubsulong]

Dear All,

I am using the code above (Thickness plugin for BoneJ) for our analysis of metallic cellular material samples. I try to figure out the further explanation of graphical representation of Tb.Th in literature but to no avail. I managed to go through the 'thickness.java' and it seems like local thickness was used as the scale to produce that yellow to blue map. Is this correct?

Any help is much appreciated.

Kind regards,

   Ayub

[Michael Doube-4]

Dear Ayub,

BoneJ uses the Fire LUT stretched to the minimum and maximum pixel values in the thickness map.

You can stretch the LUT to whatever values you like, by running this macro code:

setMinAndMax(min, max);

where min and max are the lower and upper limits respectively. Note, this only changes the LUT mapping for display and not the underlying pixel values, which still represent a thickness measurement.

Michael

> I am using the code above (Thickness plugin for BoneJ) for our analysis of
> metallic cellular material samples. I try to figure out the further
> explanation of graphical representation of Tb.Th in literature but to no
> avail. I managed to go through the 'thickness.java' and it seems like local
> thickness was used as the scale to produce that yellow to blue map. Is this
> correct?
>
> Any help is much appreciated.
>
> Kind regards,
>
>    Ayub
>
>
>
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> View this message in context: http://imagej.1557.x6.nabble.com/Thickness-plugin-3D-mapping-tp5009029.html
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>
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[ayubsulong]

Dear Michael,

Thanks for your reply. You pointed just right at the point that I wanted to look for. Thanks again.

Best regards,

   Ayub

[ayubsulong]

Dear Michael,

I have a question on how standard deviation of the strut thickness was calculated in 'thickness' command in BoneJ. How many points are taken into account for calculating the standard deviation represented in the table? or does the value came from the standard deviation of thickness of overall thicknesses of the struts in ROI of a sample.

Best regards,

   Ayub

[Michael Doube-4]

Dear Ayub

Cc:ing BoneJ list as well.

> I have a question on how standard deviation of the strut thickness was
> calculated in 'thickness' command in BoneJ. How many points are taken into
> account for calculating the standard deviation represented in the table?

All of the non-zero values in the thickness map are used to calculate the standard deviation.

If you selected 'Use ROI Manager' and the ROI Manager is populated with ROIs, the thickness map will contain only pixels from inside the ROIs. You could, in theory, calculate the standard deviation from any subset of pixels of the thickness map.

Michael


<http://www.rvc.ac.uk>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

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[ayubsulong]

Dear Michael,

Sorry for not cc:ing to BoneJ mailing list, doing it now.

I need a bit more explanation on this 'All of the non-zero values in the
thickness map are used to calculate the standard deviation.'

Imagine a thin strut within  a sample, is the thickness of the strut is
calculated on every pixel? Or does the calculation of the thickness
considered a certain spacing to avoid *too many* points. That is my
original meaning of my question 'How many points are taken...'

I need this to put them in methodology for a clear explanation in the
manuscript. Basically, I need to explain the mechanics behind the strut
measurement in the plugin.

Thanks in advance.

   Ayub


On Thursday, August 14, 2014 9:28:38 PM UTC+10, Doube, Michael wrote:

>
> Dear Ayub
>
> Cc:ing BoneJ list as well.
>
> > I have a question on how standard deviation of the strut thickness was
> > calculated in 'thickness' command in BoneJ. How many points are taken
> into
> > account for calculating the standard deviation represented in the table?
>
> All of the non-zero values in the thickness map are used to calculate the
> standard deviation.
>
> If you selected 'Use ROI Manager' and the ROI Manager is populated with
> ROIs, the thickness map will contain only pixels from inside the ROIs. You
> could, in theory, calculate the standard deviation from any subset of
> pixels of the thickness map.
>
> Michael
>
>
> <http://www.rvc.ac.uk>
>
> This message, together with any attachments, is intended for the stated
> addressee(s) only and may contain privileged or confidential information.
> Any views or opinions presented are solely those of the author and do not
> necessarily represent those of the Royal Veterinary College.
>
>

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