Overlapping Regions Info

The directory "ExtraAxonalStructures_OverlappingRegions" contains the following files:

1. combined_IntensityVolume_R1to4.nii
   Contains four combined intensity volumes from X-ray Nano-Holotomography on the vervet monkey splenium. Dim: [410 410 1532], voxel size: [375 375 375] nm
   
   
2. combined_IntensityVolume_R1to4_ExtraAxonalStructureSegmentation.nii
   Contains the segmentation of blood vessels (label 1), vacuoles (label 2) and cells (label 3) of file 1. Dim: [410 410 1532], voxel size: [375 375 375] nm
   
   
3. separateIntensityVolumes/downsampledR1.nii
4. separateIntensityVolumes/downsampledR2.nii
5. separateIntensityVolumes/downsampledR3.nii
6. separateIntensityVolumes/downsampledR4.nii
   Files 3 to 6 contain the separate intensity volumes used to create file 1. Dim: [410 410 410], voxel size: [375 375 375] nm
   
   
7. separateIntensityVolumes/fullResolutionVolumes/R1.vol
8. separateIntensityVolumes/fullResolutionVolumes/R2.vol
9. separateIntensityVolumes/fullResolutionVolumes/R3.vol
10. separateIntensityVolumes/fullResolutionVolumes/R4.vol
    Files 7 to 10 contain the full resolution XNH intensity volumes of the splenium. Dim: [2048 2048 2048], voxel size: [75 75 75] nm

The downsampled intensity volumes (files 3 to 6) in this directory are downsampled versions of overlapping X-ray Nano-Holotomography volumes of the vervet monkey splenium (files 7 to 10). They have been downsampled for the purpose of easy viewing and segmentation of large structures (e.g. cells, blood vessels) on a desktop computer. These "low resolution volumes" were downsampled to a size of 410 x 410 x 410 by extracting every 5th slice, then implementing a slice-wise downsampling by cubic interpolation and Gaussian smoothing (kernel size 5). The downsampled voxel size is 375 nm.

The overlap between consecutive volumes i.e. 1 and 2, 2 and 3, 3 and 4, is of length 13.6 µm. In the low resolution volumes of isotropic size 375 nm, this constitutes 36 voxels (rounded), and the "combined volume" (file 1) is therefore of dimensions 410 x 410 x 1532.