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ALLEN BRAIN ATLAS API

Table of Contents

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minLevel

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classtoc-style

The Allen Mouse Brain Atlas provides genome-wide in situ hybridization (ISH) image data for approximately 20,000 genes in adult mice. Each data set is processed through an informatics analysis pipeline to obtain spatially mapped quantified expression information.

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

Code Block

% Download and unzip the atlasVolume and annotation 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 annotation labels
fid = fopen('annotation.raw', 'r', 'l' );
ANO = fread( fid, prod(size), 'uint32' );
fclose( fid );
ANO = reshape(ANO,size);

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

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

Example Matlab code snippet to read in the 200 µm grid annotation volume:

Code Block

% Download and unzip the gridAnnotation zip files

% 200 micron volume size
sizeGrid = [67 41 58];
% ANOGD = 3-D matrix of grid-level annotation labels
fid = fopen( '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(34,:,:)));colormap(lines);
figure;imagesc(squeeze(ANOGD(:,:,28)));colormap(lines);

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Example Matlab code snippet to read in the 200 µm energy grid volume:

Code Block

% Download and unzip the energy grid file for Pdyn SectionDataSet

% 200 micron volume size
sizeGrid = [67 41 58];
% ENERGY = 3-D matrix of expression energy grid volume
fid = fopen('Pdyn_P56_coronal_71717084/energy.raw', 'r', 'l' );
ENERGY = fread( fid, prod(sizeGrid), 'float' );
fclose( fid );
ENERGY = reshape(ENERGY,sizeGrid);

% Display one coronal and one sagittal section
figure;imagesc(squeeze(ENERGY(34,:,:)));colormap(gray);
figure;imagesc(squeeze(ENERGY(:,:,28)));colormap(gray);

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