Histology: multiple 3D reconstruction pipeline

None

Parameters

ListOf_Staining: ListOf( String ) ( input )

Input_Volume_Reference: 3D Volume ( input )

Input_Mask: 3D Volume ( input )

Thickness: Float ( input )

Borders: ListOf( Float ) ( optional, input )

Output_Format: Choice ( input )

Output_Directory: Directory ( optional, output )

Output_ListOf_3dImage: ListOf( 3D Volume ) ( output )

Output_ListOf_3dImage_Segmented: ListOf( 3D Volume ) ( output )

Technical information

Toolbox : BrainRAT

User level : 3

Identifier : MultipleHistologicalPipeline

File name : brainvisa/toolboxes/brainrat/processes/2d-3dpmi/MultipleHistologicalPipeline.py

Supported file formats :

Input_Volume_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_Mask :

Graph and data, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Graph and data, 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

Output_ListOf_3dImage :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

Output_ListOf_3dImage_Segmented :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image