Histological slices extraction

None

Parameters

Input_Scan: Histology scan ( input )

Extraction_Scan: Histology scan ( input )

Subjects: ListOf( String ) ( input )

NumberOf_Slices_Per_Scan: Integer ( input )

NumberOf_Lines_Per_Glass_Slides: Integer ( input )

NumberOf_Columns_Per_Glass_Slides: Integer ( input )

Output_Directory: Directory ( optional, output )

Output_File: Histology scan bounding boxes ( output )

Output_Format: Choice ( input )

ListOf_Output_Image: ListOf( Histology slice ) ( output )

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : BoundingBoxGenerationPipeline

File name : brainvisa/toolboxes/bioprocessing/processes/research/toolbox/microscopy/BoundingBoxGenerationPipeline.py

Supported file formats :

Input_Scan :

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

Extraction_Scan :

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

Output_File :

JSON file, JSON file

ListOf_Output_Image :

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