Deep learning - Segmentation Model Learning

None

Parameters

Input_DataSet_File: CSV file ( optional, input )

ListOf_Input_Train_Volume: ListOf( 3D Volume ) ( optional, input )

ListOf_Input_Train_Annotations: ListOf( 3D Volume ) ( optional, input )

ListOf_Input_Validation_Volume: ListOf( 3D Volume ) ( optional, input )

ListOf_Input_Validation_Annotations: ListOf( 3D Volume ) ( optional, input )

Input_Model: 3D Volume ( optional, input )

Classes: Integer ( input )

Classes_Order: ListOf( Integer ) ( optional, input )

Dynamic_Scale_Factor: Float ( input )

Dynamic_Scale_Offset: Float ( input )

Patch_Size: ListOf( Integer ) ( input )

Pretrained: Boolean ( input )

Tile_Enabled: Boolean ( input )

Tile_Overlap: Float ( optional, input )

Epochs: Integer ( input )

Batch_Size: Integer ( input )

Batch_Size_Validation: Integer ( optional, input )

Fine_Tuning_Layers: Integer ( optional, input )

Allocate_GPUs: ListOf( Integer ) ( optional, input )

Verbose: Boolean ( input )

Output_Model: 3D Volume ( output )

Output_Model_History: Metadata Execution ( optional, output )

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : DLSegmentationModelLearn

File name : brainvisa/toolboxes/bioprocessing/processes/research/projects/segmentation/DLSegmentationModelLearn.py

Supported file formats :

Input_DataSet_File :

CSV file, CSV file

ListOf_Input_Train_Volume :

JPEG image, BMP image, GIF image, JPEG image, MNG image, PBM image, PGM image, PNG image, PPM image, TIFF image, TIFF(.tif) image, XBM image, XPM image

ListOf_Input_Train_Annotations :

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

ListOf_Input_Validation_Volume :

JPEG image, BMP image, GIF image, JPEG image, MNG image, PBM image, PGM image, PNG image, PPM image, TIFF image, TIFF(.tif) image, XBM image, XPM image

ListOf_Input_Validation_Annotations :

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_Model :

HDF5 File, HDF5 File

Output_Model :

HDF5 File, HDF5 File

Output_Model_History :

JSON file, JSON file