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Volumetric data is stored in an uncompressed format with a simple text header file in MetaImage format.

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
% ------------

% 25 micron volume size
size = [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);

% FIBT = 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);

% AVGT = 3-D matrix of average template volume
fid = fopen('averageTemplate/atlasVolume.raw', 'r', 'l' );
AVGT = fread( fid, prod(size), 'uint16' );
fclose( fid );
AVGT = reshape(AVGT,size);

% Display one coronal section
figure;imagesc(squeeze(VOL(264,:,:)));colormap(gray);
figure;imagesc(squeeze(ANO(264,:,:)));colormap(lines);
figure;imagesc(squeeze(FIBT(264,:,:)));colormap(lines);
figure;imagesc(squeeze(AVGT(264,:,:)));colormap(gray);

% Display one sagittal section
figure;imagesc(squeeze(VOL(:,:,220)));colormap(gray);
figure;imagesc(squeeze(ANO(:,:,220)));colormap(lines);
figure;imagesc(squeeze(FIBT(:,:,220)));colormap(lines);
figure;imagesc(squeeze(AVGT(:,:,220)));colormap(gray);

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

Code Block

% -----------
% Download and unzip the 100 micron gridAnnotation zip files
% -----------

%  grid volume size
sizeGrid = [133, 81, 115];

% ANOGD = 3-D matrix of grid-level annotation labels
fid = fopen( 'P56_Mouse_gridAnnotation_100micron/gridAnnotation.raw', 'r', 'l' );
ANOGD = fread( fid, prod(sizeGrid), 'uint32' );
fclose( fid );
ANOGD = reshape(ANOGD,sizeGrid);

% Display one coronal and one sagittal section
figure;imagesc(squeeze(ANOGD(73,:,:)));colormap(lines);caxis([0 3000]);
figure;imagesc(squeeze(ANOGD(:,:,78)));colormap(lines);caxis([0 3000]);

Image Alignment

As with gene expression SectionDataSets, an image synchronization service is available to find corresponding position between datasets within the Mouse Connectivity Projection product and across to datasets in the Mouse Brain and Developing Mouse Brain products.

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