Segment

volume_segment

Purpose

This utility allows you to compute the threshold that segment a desired mass. This desired mass can be expressed in voxels, daltons or aminoacids. In the latter two cases the sampling rate is needed. The segmentation is not just thresholding, but the mass is measured after the following steps:

1. Threshold the input volume at the given threshold
2. Apply morphological opening and closing to the resulting binary volume
3. The desired mass is computed as the number of voxels in the largest connected component of the volume after the morphological operations

In this way, small volumes due to noise are not taken into account during the segmentation.

The program can also be used to compute the mass remaining in the largest connected component after the described thresholding and morphological operations when a single threshold is applied.

Usage

$ volume_segment ...

Parameters

• `` Input volume to segment
• `` Mask enclosing the desired mass
• `` Desired mass expressed in voxels. This is the number of voxels which is intended to leave in the reconstruction
• `` Desired mass expressed in aminoacids. From this value and the sampling rate (that is compulsory in this case) the desired mass in voxels is computed. An average weight of 110Dalton/aminoacid is used
• `` Desired mass expressed in daltons. From this value and the sampling rate (that is compulsory in this case) the desired mass in voxels is computed. An average weight of 1.207Angstrom^3/Dalton is used.
• `` Sampling rate inAngstrom/pixel
• `` Use this threshold
• `` Use Entropy Otsu's method
• -wang [r3] = Radius for a Wang smoothing (convolution with a Gaussian; but only positive values participate in the convolution)
• `` Calculate probabilistic solvent mask

Examples and Notes

• Cannot find threshold Sometimes there are two large components in the volume. In these cases it is difficult to find a threshold that provides the desired mass since either of two: or the two pieces are disconnected and then the mass is too small or the two pieces are connected and then the mass is too large

Compute the threshold for a mass of 600 aminoacids when images are sampled at 3.5A/pix

$ volume_segment -i volume.vol -o mask.vol -aa_mass 600 -sampling_rate 3.5

Compute the threshold for a mass of 60000 Dalton when images are sampled at 3.5A/pix

$ volume_segment -i volume.vol -o mask.vol -dalton_mass 60000 -sampling_rate 3.5

Compute the threshold for a mass of 38000 voxels

$ volume_segment -i volume.vol -o mask.vol -voxel_mass 38000

Compute the mass in the largest connected piece for a threshold equal 0.5

$ volume_segment -i volume.vol -o mask.vol -threshold 0.5 

Segment the volume using Entropy-Otsu method (the result may not be a singly connected component)

$ volume_segment -i volume.vol -o mask.vol -otsu

--Main.AlfredoSolano - 30 Jan 2007