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, 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

Extraction_Scan :

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

Output_Directory :

Directory, Directory

Output_File :

JSON file, JSON file

ListOf_Output_Image :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image