IndividualizingAndStackingMultipleSlices

This process provides a fully automated procedure for extraction and individualization of histological or autoradiographic slices from overall scans, using histogram analysis, threshold and iterative mathematical morphology operations. The individualized slices are then stacked in the direction orthogonal to the cut-plane. Slices are arranged in the sectioning process order, hence in a continuous antero-posterior relationship. This process initializes the following 3D reconstruction by stacking these slices according to their gravity centre parameters (centering procedure).

If you have any problems with your data, please check the procedure described in the How To Scan section.

NOTE: Make sure to process an animal after another as well as a post mortem imaging modality after another. For instance, start by processing all overall scans of histological sections of rat n° 1. Resume processing on all overall scans of autoradiographic sections of the same animal. Then, move to rat n° 2 and repeat these two steps.

Parameters

Input_ListOf_2dImage: ListOf( 2D Image ) ( input )

Click on , for instance Test_rat1_cresyl_col1_sec42.tif, Test_rat1_cresyl_col2_sec36.tif, Test_rat1_cresyl_col3_sec42.tif and Test_rat1_cresyl_col4_sec42.tif.
Select all overall scans to be processed by holding down on the control button on your keyboard (Ctrl).

Input_ListOf_2dImage_Preprocessed: ListOf( 2D Image ) ( optional, input )

Click on .
Select all overall scans which have been needed to be pre-processed (Cf. How To Scan) by holding down on the control button on your keyboard (Ctrl).

Scanner_Resolution: Integer ( input )

Enter the in-plane digitization resolution in dpi (dot per inch) of your flatbed scanner.

Threshold_Computation: Choice ( input )

Specify the threshold computation mode. It can be determined, either automatically, either manually by filling Low_Threshold and High_Threshold parameters.

Glass_Slide_Order: Choice ( input )

Choose the arrangement in which the glass slides have been exposed to an autoradiographic film or laid down on the surface of the scanner: top-bottom or bottom-top.

Global_Glass_Slide_Filling: Choice ( input )

Choose the global arrangement slices on glass slides: according to line or to column first (Cf. How To Scan).

Local_Glass_Slide_Filling: Choice ( input )

Choose the local arrangement slices on glass slides (Cf. How To Scan).

ListOf_NumberOf_Slices_Per_Scan: ListOf( Integer ) ( input )

Enter the number of slices contained in each overall scan. Separate them from each other by pressing the space bar.

ListOf_NumberOf_Lines_Per_Glass_Slides: ListOf( Integer ) ( input )

Enter the number of lines according which the slices have been arranged on glass slides in each overall scan. Separate them from each other by pressing the space bar.

ListOf_NumberOf_Columns_Per_Glass_Slides: ListOf( Integer ) ( input )

Enter the number of columns according which the slices have been arranged on glass slides in each overall scan. Separate them from each other by pressing the space bar.

ListOf_Minimum_Slice_Surface: ListOf( Integer ) ( input )

Enter the surface (in mm²) of the shortest slices in each overall scan. Separate them from each other by pressing the space bar.
In rat, this surface is of about 5 mm² for olfactory bulb sections, 10-20 mm² of frontal brain sections (frontal cortex, etc.), 50-100 mm² for midbrain sections (striatum, hippocampus, thalamus, colliculus, etc.) and 20 mm² for cerebellum sections.

Dimension_X: Integer ( input )

Enter the horizontal dimension (in number of pixels) of the final stacked volume.

Dimension_Y: Integer ( input )

Enter the horizontal dimension (in number of pixels) of the final stacked volume.

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 : IndividualizingAndStackingMultipleSlices

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

Input_ListOf_2dImage_Preprocessed :

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