StackingIndividualSlices

This process enables the stacking of individually digitized slice images in the direction orthogonal to the cut-plane. Slices are arranged in the order in which they were selected (see comments on parameter Input_ListOf_2dImage). This process initializes the following 3D reconstruction by stacking these slices according to their gravity centre parameters (centering procedure).

The process operates with individual images having different horizontal and vertical dimensions. However, make sure that all the slice images were digitized with the same in-plane digitization resolution.

Parameters

Input_ListOf_2dImage: ListOf( 2D Image ) ( input )

Click on .
Select the multiple slice images to be stacked by holding down on the control button on your keyboard (Ctrl), for instance Test_rat1_cresyl_slice001.tif, Test_rat1_cresyl_slice002.tif, Test_rat1_cresyl_slice003.tif ... Test_rat1_cresyl_slice162.tif.

Dimension_X: Integer ( optional, input )

Enter the horizontal dimension (in number of pixels) of the final stacked volume. This parameter is optional, if you do not complete it, the final horizontal dimension of the stacked volume will be based on the horizontal dimension of the largest image in the series.

Dimension_Y: Integer ( optional, input )

Enter the vertical dimension (in number of pixels) of the final stacked volume. This parameter is optional, if you do not complete it, the final vertical dimension of the stacked volume will be based on the vertical dimension of the largest image in the series.

Scanner_Resolution: Integer ( input )

Enter the in-plane resolution in dpi (dot per inch) of your digitizing system (flatbed scanner, CCD camera, ...).
A default value of 600 dpi, corresponding to ~42µm, is automatically assigned.

Inter_Slice_Thickness: Float ( input )

Enter the interslice interval, i.e. the distance in mm between two consecutive slices in the final stack, for instance 0.02 (20 µm = 0.02 mm).

NOTE: if you have acquired one out three 20 µm-thick sections, the interstice interval will be 0.02*3=0.06 mm.

Output_3dImage: 3D Volume ( output )

Click on
Specify the output directory where the stack volume will be written and enter the output file name, for instance Test_stack_rat1_cresyl.ima

Technical information

Toolbox : BrainRAT

User level : 0

Identifier : StackingIndividualSlices

File name : brainvisa/toolboxes/brainrat/processes/2d-3dpmi/StackingIndividualSlices.py

Supported file formats :

Input_ListOf_2dImage :

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_3dImage :

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