3D volume quantification

[Mauricio Aguirre Morales]

Dear Fiji Community

This is actually the first time I post on a forum, thus I don´t know the
mechanics very well. I am trying to determine the volume of fungal hypha
over mineral particles. For this I have acquired images stacks with a
multiphoton microscopy and have built 3D models with the Fiji. I am
using the scale bar tools for microscopes to adjust the scale according
to the features of the microscope but this option in this program only
limits to 2D. However, when I select the 2D scale for a given image and
calculate the 3D volume the out coming result is given in cubic
micrometers. My question is how to correct or specify the scale in the Z
axis since the microscope allows changing the space between the layers
of the stack and of course the volume would change.

Sincerely
Mauricio Aguirre Morales

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[dscho]

Hi Mauricio,

On Tue, 2 Sep 2014, Mauricio Aguirre Morales wrote:

> My question is how to correct or specify the scale in the Z axis since
> the microscope allows changing the space between the layers of the stack
> and of course the volume would change.

You can change the "voxel depth" (which is really the z distance between
pixels) using Image>Properties... (Ctrl+Shift+P is the keyboard shortcut).

Ciao,
Johannes

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