Extract connected components in order

This process propose to extract connected components of a binary data volume in the selected order.
It enables to order the extracted components int the coronal, sagittal and axial plane.

Figure 1: Section arrangements on different planes (coronal, sagittal and axial).


Figure 2: All possible section arrangement on the coronal plane according to X axis first.


Figure 3: All possible section arrangement on the coronal plane according to Y axis first.


Figure 4: the 3D arrangement of the coronal plane.

Parameters

Input_Binary_Volume: 3D Volume ( input )

Upload the binary data volume

Number_Of_Components: Integer ( input )

Enter the number of components to be extracted

Plane: Choice ( input )

Select the plane of arrangement (coronal, sagittal or axial) in which the components have been arranged (Figure 1)

Global_Arrangement: Choice ( input )

Choose the global arrangement on plane (Figure 2 and 3)

Local_Arrangement: Choice ( input )

Choose the local arrangement on plane (Figure 2 and 3)

Plane_Order: Choice ( input )

Select the 3D arrangement of plane (Figure 4)

Number_Of_Components_X: Integer ( input )

Enter the number of components on the X-axis

Number_Of_Components_Y: Integer ( input )

Enter the number of components on the Y-axis

Number_Of_Components_Z: Integer ( input )

Enter the number of components on the Z-axis

Output_Label_Volume: 3D Volume ( output )

Specify the output directory and enter the output file name.

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : ExtractComponentsInOrder

File name : brainvisa/toolboxes/bioprocessing/processes/research/toolbox/ExtractComponentsInOrder.py

Supported file formats :

Input_Binary_Volume :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

Output_Label_Volume :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image