Bug in quantification module label command?

[JPSuuronen]

Hi all,

It seems that the label command in the thresholding command group of Quantification tools module (Avizo fire, it seems to be the case in at least v6.2,6.3 and 7.0) does not work properly.

I have binary data representing a skeletonized fiber 'network', from which I'm trying to calculate the orientations of individual fibers with the I_analyze command. However, the labeling step seems to be splitting some of the fibers in several sections with no apparent reason. E.g. the tracelines module of Xskeleton pack does not find a node at these locations.

I could work around the problem by labeling the data first with Matlab, and then casting the result to Visilog labels via the command
'quantification tools'->'miscellaneous'->'convert'.
Running I_analyze on the result of this will skip the labeling step and give the correct result. This adds some unnecessary extra steps to the analysis, however.

Is the label command just arbitrarily missing some connections in the data or using some other definition for connectivity than the 26-neighborhood? (manually switching to a 26-neighborhood with 'quantification tools' -> 'morphology' -> 'neighbourhood' does not help).

Regards,

J-P

[noesis]

Hello J.P

Could you post a crop of your image where you see a problem ?

Thank you

Laurent

[JPSuuronen]

Hello Laurent,

and thanks for your reply.

I attached three datasets:

image.am is a small portion of my (binary) data, consisting of one whole and three tiny pieces of a fiber skeleton (one maybe only a single voxel).

image_visiloglabels.am is the output of quantification module's label-command

image_matlablabels.am is obtained with this code

image_matlablabels = uint16(bwlabeln(A));
clear A;

in the CalculusMATLAB module (bwlabeln is a function from MATLAB's Image Processing Toolbox).

As you can see, the quantification module command splits the longest fiber in three, and I can't figure out why... (Using Avizo Fire 7.0.0, at the moment).

Cheers,
J-P

[noesis]

Hello

I confirm there is a mystery with your dataset.
We will try to correct it as soon as possible.

Best regards

Laurent

[noesis]

Hello

I confirm, there is a bug.
This problem is now fixed with the last service pack of Visilog 7 (7.0.1.4)

and it will be fixed with a next release of Avizo

Very sorry for this error.

Laurent