Histology : 3d reconstruction pipeline

None

Parameters

Input_ListOf_2dImage: ListOf( 2D Image ) ( input )

Input_ListOf_2dPhoto_Reference: ListOf( 2D Image ) ( input )

Input_BoundingBox: Text file ( input )

Input_Learning_Set: Text file ( input )

Class_Background: Choice ( input )

Channel_Histo: Choice ( input )

Channel_Photo: Choice ( input )

Number_Of_Components: Integer ( input )

Thickness: Float ( input )

Output_Prefix: String ( input )

Output_Directory: Directory ( input )

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : 3DHistoProcess

File name : brainvisa/toolboxes/bioprocessing/processes/research/2d-3dpmi/3DHistoProcess.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_ListOf_2dPhoto_Reference :

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_BoundingBox :

Minf, Minf

Input_Learning_Set :

Text file, Text file

Output_Directory :

Directory, Directory