Delete backgroung and manual 3D volume rendering

[PedroFernandez]

To whom it may concern,

I am trying to segregate a .tiff file (over 700 slides) and I would like to separete the outer black point. When I aply a threshold filter for the darkest colours, Avizo identify outer zones as porosity and, it isn´t true. Anybody can help me to separate the real porosity from the false one??

Another question related to the previous one. I would like to made a 3D volume rendering of the whole sample and, again, I have the problem of the outher zones. I have tried to create a manual 3D volume (cilinder, box...), but I would like to create a 3D volume that will be adjust to the edges of my sample. Can anybody help me with this??

I woukld be delighted if anybody could help me with any of this situations.

[shuom]

The way I deal with this is using the 'Volume Edit' module from the 'compute' submenu. I use a tabbox to select the data I want, and then change the padding value to '255' (White), and cut the outer area. That creates a new dataset. However, the top slice and the bottom slice have issues.

Hope this helps.

[PedroFernandez]

Dear Shuom,

Really thanks for your quickly response. I apreciate it.

I have been testing it and, although the histogram has been reduced, it doesn´t work.

I show you, at the file that I have attached, what happen when I try to segregate the porosity (blackest pixeles). A cover has been developed over the edge (2D at this point) between outside and inside, which don´t let me to cuantificate the porosity at the right way.

I have been trying by filtering, other segmentation tools (I have created subboxes and it works, but I want to study the whole sample, not just a fraction of this)... even aritmethic ecuations, but I can get waht I want.

Do you think I could do what I want from another way?

[barbis]

Hello!

This looks like a good sample for some heavy anisotropic diffusion filtering before a global threshold.

maybe it helps!

[PedroFernandez]

Hi barbis!!

Thanks for your suggestion

I have fixed the problem.
I have used some filters (median smoothing and anisotrophic diffusion) before the applycation of several 3D Quantification operations.

Really thanks for your support my friends!!