Histology: 3D reconstruction pipeline

None

Paramètres

Staining: String ( input )

Input_ListOf_2dImage: ListOf( 2D Image ) ( input )

Input_Volume_Reference: Volume 3D ( entrée )

Input_Mask: Volume 3D ( entrée )

Input_Model: Text file ( optional, entrée )

Selection: ListOf( Choice ) ( optional, input )

Resolution: Entier ( optional, input )

Pixel_Size: Réel ( optional, input )

Thickness: Réel ( input )

Borders: ListOf( Réel ) ( optional, input )

Output_Format: Choice ( input )

Output_Directory: Répertoire ( sortie )

Output_Volume: Volume 3D ( sortie )

Output_Volume_Segmented: Volume 3D ( sortie )

Informations techniques

Toolbox : BrainRAT

Niveau d'utilisateur : 3

Identifiant : HistologicalPipeline

Nom de fichier : brainvisa/toolboxes/brainrat/processes/2d-3dpmi/HistologicalPipeline.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_Volume_Reference :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Répertoire, 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, Répertoire, 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

Input_Model :

Text file, Text file

Output_Directory :

Répertoire, Répertoire

Output_Volume :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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_Volume_Segmented :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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