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Code Block
    % Download and unzip the density grid file for VISp SectionDataSet

    % 100 micron volume size
    sizeGrid = [133 81 115];
    % DENSITY = 3-D matrix of projection density grid volume
    fid = fopen('density.raw', 'r', 'l' );
    DENSITY = fread( fid, prod(sizeGrid), 'float' );
    fclose( fid );
    DENSITY = reshape(DENSITY,sizeGrid);

    % Display one coronal and one sagittal section
    figure;imagesc(squeeze(DENSITY (95,:,:)));caxis([0,1]);colormap(hot);
    figure;imagesc(squeeze(DENSITY (:,:,72)));caxis([0,1]);colormap(hot);


    

Projection Structure Unionization

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Example Matlab code snippet to upsample gene expression grid with "no data" handling:    % Download and unzip energy volume file for gene Rasd2 coronal SectionDataSet 73636089
   

Code Block

    % Download and unzip energy volume file for gene Rasd2 coronal SectionDataSet 73636089
    mkdir('Rasd2_73636089');

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    urlwrite('http://api.brain-map.org/grid_data/download/74819249?include=density', 'temp.zip');

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    unzip('temp.zip','Rasd2_73636089');

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    % Download and unzip density volume file for BLAa injection SectionDataSet 113144533
    mkdir('BLAa_113144533');

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    urlwrite('http://api.brain-map.org/grid_data/download/113144533?include=density', 'temp.zip');

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    unzip('temp.zip','BLAa_113144533');

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   % Gene expression grids are at 200 micron resolution.

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    geneGridSize = 

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[67 41 58

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];

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    fid = fopen('Rasd2_73636089/density.raw', 'r', 'l'

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  );

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    Rasd2 = fread( fid, prod(geneGridSize), 'float' );

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    fclose(fid);

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    Rasd2 = reshape( Rasd2, geneGridSize );

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   % Projection grids are at 100 micron 

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resolution
    projectionGridSize = 

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[133 81 115

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];

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    fid = fopen('BLAa_113144533/density.raw', 'r', 'l'

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  );

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    BLAa = fread( fid, prod(projectionGridSize), 'float' );

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    fclose(fid);

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    BLAa = reshape( BLAa, projectionGridSize );

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   % Upsample gene expression grid to same dimension as projection grid using linear 

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interpolation
    [xi,yi,zi

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] = meshgrid(1:0.5:41,1:0.5:67,1:0.5:58); %note: matlab transposes x-y

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    d = Rasd2; d(d<0) = 0; % fill in missing data as zeroes

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    Rasd2_100 = interp3(d ,xi,yi,zi,'linear');

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    % Handle "no data" (-1) voxels.

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    % Create a mask of "data" vs "no data" voxels and apply linear

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 interpolation
    m = (Rasd2  >= 0); mi = interp3(m,xi,yi,zi,'linear');

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    % Normalize data by dividing by interpolated mask. Assign value of "-1" to "no data" voxels.

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    Rasd2_100 = Rasd2_100 ./ mi;

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    Rasd2_100( mi <= 0 ) = -1;

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   % Create a merged image of one coronal plane;

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    gimg = squeeze(Rasd2_100(52,:,

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:)); gimg = max(0,gimg); gimg = gimg / 0.025; gimg = min(1,gimg);

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    pimg = squeeze(BLAa(52,:,

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:)); pimg = max(0,pimg); pimg = pimg / 0.8; pimg = min(1,pimg);

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    rgb = zeros(

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[size(gimg),3

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]); rgb(:,:,1) = gimg; rgb(:,:,2) = pimg;

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    figure; image(rgb);

Image Removed

Figure: ISH SectionDataSet (id=73636089) for gene Rasd2 showing enriched expression in the striatum (left). Projection SectionDataSet (id=73636089) with injection in the anterior part of the basolateral amygdalar nucleus (BLAa) showing projection to the striatum and other brain areas (center). One coronal slice of the BLAa projection density grid (green) merged with an upsampled and interpolated Rasd2 expression density grid (red).