Separate_objects

Separate objects

Purpose

This utility allows you to separate different disconnected objects in a binary volume. In this way, small objects can be separated from large ones in reconstructions. This is very useful for reconstructions. Objects are written in separate files as binary volumes, too. Ouput volume number 0 is the background, number 1 corresponds to object 1, number 2 to object 2 ...

This program also tells you the number of voxels on each object.

Usage

$ separate_objects ...

Parameters

• `` segments a binary volume and saves each region in the input volume in a new binary volume with the same size than the input . The volume names are[fnroot]_out?????.vol
• `` If no output root name is given then the root name of the input volume is used
• `` The binary masks are inverted
• -min_size [size0] = Only the volumes with size (number of voxel different from 0) bigger than size are saved

Examples and notes

Cleaning a volume and selecting the threshold of 100% of mass

# Apply threshold to the input density_volume, in this case the threshold is 0
$ xmipp_threshold -i density_volume.vol -o binary_volume.vol -binarize -below 0

# Clean the binary volume
$ xmipp_morphology -i binary_volume -ope
$ xmipp_morphology -i binary_volume -clo

# Count voxels in each object to select the appropriate threshold
# Play with threshold until the desired amount of voxels are
# gathered in a single object
# Do not save the volume is the object size is smaller than 100
$ xmipp_separate_objects -i binary_volume -min_size 100

# Dilate the mask a little and apply it to input volume
$ xmipp_morphology -i binary_mask00001.vol -dil
$ xmipp_mask -i density_volume.vol -o clean_density_volume.vol -mask binary_mask00001.vol 

--Main.AlfredoSolano - 30 Jan 2007