Measuring volume and area

[mtvinas]

Hi again,

I'm working with a FIB tomography, and I've labelled 3 different phases.
I'm trying to get volume and area information.

For volume I used MaterialStatistics module to get the volume of different phases. The sum of volumes of different phases has to be the total volume (1,12E12 in my case).
Then, I used the Quantification module "volume3d". In this case, only the total volume appears, but in this case is 2,29E12.

I used the QuantificationThreshold to separate the different values in different binary images, and used "volume3d" again for each image.
In this case, volume3d shows the same value as "MaterialStatistics".

So I have something like this:

FIBSLICE.Labels.am 2.900765e+012
phase1.thresholded 6.525787e+011
phase2.thresholded 4.714861e+011
phase3.thresholded 56202240

There are only this 3 phases, but the sum of phase1+phase2+phase3 is not equal to the general "FIBSLICE.Labels".

Why?
What I am doing wrong?

On the other hand, I'm trying to get the areas and specific surface.
The problem is that I can't do this with labelled (or segmented) image: I have to do with thresholded images (one binary image for each phase). Is this correct?
I am using the Quantification module "area3d".

A better user guide for xQuant pack would be nice.

Thanks.
Regards.

[barbis]

Do you have 3 phases + exterior, that is, the background?
Could the background volume account for the missing volume?
If not, i would recommend to create a simple image with spheres with known areas
and volumes and intensities. Then compare the results to the analytical ones...

[mtvinas]

Hi,
Thank you, barbis, you're right.
That was exactly the problem: I wasn't counting the "exterior" label.
It's odd, because in "MaterialStatistics" module, Exterior label appears as "Count: 0" and "Volume: 0".
But the difference between those values is exactly the total volume of the 3D cube, so that's it.

Thanks again!

Besides that: there is anywhere a guide for xQuant pack (Quantification module)? I'm in troubles and spending a lot of time trying to guess what are the meaning of each value -- the tutorials only covers a very little part of this module.

[noesis]

Hello

Did you read refguide.pdf book ?
You can find all informations inside this manual.

Other way, VSG proposes specific training for XQuant.

Laurent

[mtvinas]

Hello,

I didn't see this refguide.pdf.
I think this is what I need to understand the different commands.

Thank you!

[noesis]

On Seven:

C:\Programmes\Avizo-7\doc\Visilog\refguide.pdf

or press F1 when a command is selected on XQuant module

[mtvinas]

Thank you!