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, 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

Input_ListOf_2dPhoto_Reference :

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

Input_BoundingBox :

Minf, Minf

Input_Learning_Set :

Text file, Text file

Output_Directory :

Directory, Directory