Histology scan

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Inheritance graph

Defined in file : brainvisa/toolboxes/bioprocessing/types/biology.py

Used in the following processes

Automatic bounding boxes detection
CZI only: Automatic extract meta-data bounding boxes
Histological slices extraction
{Importer} Histology scan

Associated formats

Aims readable volume formats
Aperio svs
BMP image
DICOM image
Directory
ECAT i image
ECAT v image
FDF image
FreesurferMGH
FreesurferMGZ
GIF image
GIS image
gz compressed MINC image
gz compressed NIFTI-1 image
Hamamatsu ndpi
Hamamatsu vms
Hamamatsu vmu
JPEG image
Leica scn
MINC image
NIFTI-1 image
PBM image
PGM image
PNG image
PPM image
Sakura svslide
SPM image
TIFF image
TIFF(.tif) image
Ventana bif
VIDA image
XBM image
XPM image
Zeiss czi

Associated ontology rules

  • brainvisa-3.2.0 :
    • {study}/{center}/histology/{scan_session}/scans/{marker}/{specie}_<marker>_serie{serie}_scan{scan_number}_level{extracted_level}

    Key attributes

  • brainvisa-3.2.0 :
    • study ,  center ,  scan_session ,  marker ,  specie ,  serie ,  scan_number ,  extracted_level