XNH Info

The folder "XNH datasets" contains the following 2 directories:

1. "axonSegmentations"
   This directory contains X-ray Nano-Holotomography volumes of the monkey brain splenium, (referred to as "region 1" or "R1" in the context of other volumes included in this data package), and the segmentations of 54 axons from that volume.
   
   
2. "extraAxonalStructures_OverlappingRegions"
   This directory contains X-ray Nano-Holotomography volumes of four overlapping regions of the monkey brain splenium, and the segmentation of cell clusters, blood vessels and vacuoles from the "extended" volume.

The XNH intensity volumes are either provided as the original .VOL files (approximately 32 GB each) or downsampled .NII files for viewing on a standard desktop computer. The volumes are acquired such that the z-axis represents the left-right axis of the vervet monkey brain. The orientation of the x- and y-axes is unknown.

Due to their size, loading the entire .VOL volumes is memory intensive. Below, we include an example of how a number of slices, n_slices, of the volume can be loaded in MATLAB. Here, the variables are as follows: "filename": path to .VOL file "n_slices": number of slices to load "start_slice": slice from which to start reading XNH intensity volume

% ---- MATLAB Load .VOL example ---- %

filename = 'R1.vol';
n_slices = 2048;
start_slice = 1; % start reading matrix from start_slice

% Load image in matrix I
dim = [2048 2048 n_slices];
fid = fopen(filename);
fseek(fid, dim(1)*dim(2)*(start_slice-1)*4, 'bof');
I = fread(fid,dim(1)*dim(2)*dim(3),'single');
I = reshape(I,[dim(1) dim(2) dim(3)]);