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Voxel Resolution

Volume Dimension (AP,SI,LR)

10 micron isotropic 10µm sotropic

1320, 800, 1140

25 micron 25µm isotropic

528, 320, 456

50 micron 50µm isotropic

264, 160, 228

100 micron 100µm isotropic

132, 80, 114

All volumetric data is compressed NRRD (Nearly Raw Raster Data) format. The raw numerical data is stored as a 1-D array raster as shown in the figure below.

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Example Matlab code snippet to read in the 25µm atlas and annotation volumes:

Code Block
% ------------
% Download and unzip the atlasVolume, annotation, annotationFiber and averageTemplate zip files
% -------------------
%
% 25Download microna volumeNRRD sizereader
size% =For [528 320 456];

% VOL = 3-D matrix of atlas Nissl volume
fid = fopen('atlasVolume/atlasVolume.raw', 'r', 'l' );
VOL = fread( fid, prod(size), 'uint8' );
fclose( fid );
VOL = reshape(VOL,size);

% ANO = 3-D matrix of structural annotation labels
fid = fopen('P56_Mouse_annotation/annotation.raw', 'r', 'l' );
ANO = fread( fid, prod(size), 'uint32' );
fclose( fid );
ANO = reshape(ANO,size);

% FIBTexample:
% http://www.mathworks.com/matlabcentral/fileexchange/34653-nrrd-format-file-reader
%
% Requires: MATLAB 7.13 (R2011b)
%
% Download average_template_25.nrrd,
%          ara_nissl_25.nrrd,
%          ccf_2015/annotation_25.nrrd
%
% ---------------------------------

%
% Read image volume with NRRD reader
% Note that reader swaps the order of the first two axes
%
% AVGT = 3-D matrix of fiber tract annotation labels
fid = fopen('P56_Mouse_annotationFiber/annotationFiber.raw', 'r', 'l' );
FIBT = fread( fid, prod(size), 'uint32' );
fclose( fid );
FIBT = reshape(FIBT,size);

% AVGTaverage_template
% NISSL = 3-D matrix of ara_nissl
% ANO = 3-D matrix of average template volume
fidccf_2015/anntotation
%
[AVGT, metaAVGT] = fopennrrdread('averageTemplate/atlasVolume.raw', 'r', 'l' );
AVGT = fread( fid, prod(size), 'uint16' );
fclose( fid );
AVGT = reshape(AVGT,size);

average_template_25.nrrd');
[NISSL, metaNISSL] = nrrdread('ara_nissl_25.nrrd');
[ANO, metaANO] = nrrdread('annotation_25.nrrd');


% Display one coronal section
figure;imagesc(squeeze(VOLAVGT(:,264,:,:)));colormap(gray(256)); axis equal;
figure;imagesc(squeeze(ANONISSL(:,264,:,:)));colormap(linesgray(256)); axis equal;
figure;imagesc(squeeze(FIBTANO(:,264,:,:)));colormap(lines
caxis([1,2000]); figure;imagesccolormap(squeeze(AVGT(264,:,:lines(256)));colormap(gray); axis equal;

% Display one sagittalsagttial section
figure;imagesc(squeeze(VOLAVGT(:,:,220)));colormap(gray(256)); axis equal;
figure;imagesc(squeeze(ANONISSL(:,:,220)));colormap(linesgray(256)); axis equal;
figure;imagesc(squeeze(FIBTANO(:,:,220)));colormap(lines
caxis([1,2000]); figure;imagesccolormap(squeeze(AVGT(:,:,220lines(256)));colormap(gray); axis equal;

Example Matlab code snippet to read in the 100µm grid annotation volume:

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