Photo : 3d reconstruction pipeline

Parameters

Input_ListOf_2dImage: ListOf( 2D Image ) ( input )

Select all overall photos to be processed

Input_Learning_Set: Text file ( input )

Select the learning file for photo segmentation. If this file doesn't existe, you must generate one using biovision pipeline

Class_Background: Choice ( input )

Class_Foreground: Choice ( input )

Number_Of_Components_Per_Line: Integer ( input )

Enter the number of components arranged in a line

Number_Of_Components_Per_Column: Integer ( input )

Enter the number of components arranged in a column

Calibration: Boolean ( input )

Choice one of the following options :

1. Do not use : if it is not necessary to calibre
2. Use existing one : if the calibration file existe
3. Generate one : if the calibration file doesn't existe

__inputCalibration_Image: 2D Image ( input )

__Horizontal_calib_LEFT: Point3D ( input )

__Horizontal_calib_RIGHT: Point3D ( input )

__Vertical_calib_TOP: Point3D ( input )

__Vertical_calib_DOWN: Point3D ( input )

__distanceHorizontalMillimeter: Float ( input )

__distanceVerticalMillimeter: Float ( input )

Thickness: Float ( input )

Enter the thickness value of voxel z dimension (default : 1.0)

Flip: Choice ( input )

Separation_mode: Choice ( input )

Output_Prefix: String ( input )

Enter the prefix that will be used to create the individual output volumes

Output_Directory: Directory ( input )

Specify the output directory in which the results of process will be stored

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : PhotoPipeline

File name : brainvisa/toolboxes/bioprocessing/processes/research/photoreference/PhotoPipeline.py

Supported file formats :

Input_ListOf_2dImage :

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

Input_Learning_Set :

Text file, Text file

__inputCalibration_Image :

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

Output_Directory :

Directory, Directory