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ALLEN BRAIN ATLAS API

Table of Contents

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The Allen Developing Mouse Brain Atlas provides in situ hybridization (ISH) image data for approximately 2,000 genes over embryonic and postnatal timepoints. Each data set is processed through an informatics analysis pipeline to obtain spatially mapped quantified expression information.

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The atlas volume dimension and resolution for each ReferenceSpace vary with age, scanning platform and gene sampling density as listed in the table below.

ReferenceSpace

Age

Anatomy

atlasVolume Dimension

atlasVolume Resolution

1

E11.5

Embryo

[345,371,158]

[16.0,16.0,20.0]

2

E13.5

Embryo

[552,673,340]

[16.0,16.0,20.0]

3

E15.5

Embryo

[704,982,386]

[16.0,16.0,20.0]

4

E16.5

Head

[704,982,386]

[16.0,16.0,20.0]

5

E18.5

Brain

[581,370,278]

[16.0,16.0,20.0]

6

P4

Brain

[724,403,398]

[16.752,16.752,20.0]

7

P14

Brain

[794,469,390]

[16.752,16.752,25.0]

8

P28

Brain

[863,480,418]

[16.752,16.752,25.0]

9

P56

Brain

[528,320,456]

[25.0,25.0,25.0]

10

P56

Brain

[528,320,456]

[25.0,25.0,25.0]

Table information in CSV format.

The grid dimension and resolution for each ReferenceSpace vary with age and gene sampling density as listed in the table below.

ReferenceSpace

Age

Anatomy

grid Dimension

grid Resolution

1

E11.5

Embryo

[70,75,40]

[80.0,80.0,80.0]

2

E13.5

Embryo

[89,109,69]

[100.0,100.0,100.0]

3

E15.5

Embryo

[94,132,65]

[120.0,120.0,120.0]

4

E16.5

Head

[94,132,65]

[120.0,120.0,120.0]

5

E18.5

Brain

[67,43,40]

[140.0,140.0,140.0]

6

P4

Brain

[77,43,50]

[160.0,160.0,160.0]

7

P14

Brain

[68,40,50]

[200.0,200.0,200.0]

8

P28

Brain

[73,41,53]

[200.0,200.0,200.0]

9

P56

Brain

[67,41,58]

[200.0,200.0,200.0]

10

P56

Brain

[67,41,58]

[200.0,200.0,200.0]

Table information in CSV format.

Example Matlab code snippet to read in the P4 atlas and annotation volume:

Code Block

% ------------
% Download and unzip the P4 (ReferenceSpace=6) atlasVolume and annotation zip files
% ------------

% atlas volume size
size = [724,403,398];

% VOL = 3-D matrix of atlas Nissl volume
fid = fopen('P4_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('P4_DevMouse2012_annotation/annotation.raw', 'r', 'l' );
ANO = fread( fid, prod(size), 'uint32' );
fclose( fid );
ANO = reshape(ANO,size);

% Display one coronal section
figure;imagesc(squeeze(VOL(362,:,:)));colormap(gray);
figure;imagesc(squeeze(ANO(362,:,:)));colormap(lines);

% Display one sagittal section
figure;imagesc(squeeze(ANO(:,:,115)));colormap(lines);
figure;imagesc(squeeze(VOL(:,:,115)));colormap(gray);

Example Matlab code snippet to read in the P4 grid annotation volume:

Code Block

% -----------
% Download and unzip the P4 (ReferenceSpace=6) gridAnnotation zip files
% -----------

%  grid volume size
sizeGrid = [77,43,50];

% ANOGD = 3-D matrix of grid-level annotation labels
fid = fopen( 'P4_DevMouse2012_gridAnnotation/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(36,:,:)));colormap(lines);
figure;imagesc(squeeze(ANOGD(:,:,14)));colormap(lines);

...

Example Matlab code snippet to read an energy grid volume:

Code Block

%------------
% Download and unzip the energy grid file for P4 Rora Pdyn SectionDataSet
% -----------

%  grid volume size
sizeGrid = [77,43,50];

% ENERGY = 3-D matrix of expression energy grid volume
fid = fopen('Rora_P4_sagittal_100054927/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(36,:,:)));colormap(gray);
figure;imagesc(squeeze(ENERGY(:,:,14)));colormap(gray);

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