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- All experiments in the "Mouse Connectivity Projection" Product
- All experiments with an injection in the primary visual area (VISp, structure_id=385)
- Detailed metadata for one experiment with injection in the VISp (id=126862385) (http://api.brain-map.org/api/v2/data/query.xml?criteria=model::SectionDataSet,rma::criteria,[id$eq126862385],rma::include,specimen\(stereotaxic_injections\(primary_injection_structure,structures,stereotaxic_injection_coordinates\)\),equalization,sub_images,rma::options[order$eq'sub_images.section_number$asc'])
Figure: Projection dataset (id=126862385) with injection in the primary visual area (VISp) as visualized in the web application image viewer.
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In the web application, images from the experiment are visualized in an experimental detail page. All displayed information, images and structural projection values are also available through the API.
Figure:Experiment detail page for an injection into the primary visual area.
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All SectionDataSets are registered to ReferenceSpace id = 9 in PIR orientation (+x = posterior, +y = inferior, +z = right).
Figure: The common reference space is in PIR orientation where x axis = Anterior-to-Posterior, y axis = Superior-to-Inferior and z axis = Left-to-Right.
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- Sync a VISp and VISal experiment to a location in a SCs SectionDataSet
- Sync the P56 coronal reference atlas to a location in the SCs SectionDataSet
Figure: Point-based image synchronization. Multiple image-series in the Zoom-and-Pan (Zap) viewer can be synchronized to the same approximate location. Before and after synchronization screenshots show projection data with injection in the superior colliculus (SCs), primary visual area (VISp) anteolateral visual area (VISal), and the relevant coronal plates of the Allen Reference Atlas. All experiments show strong signal in the thalamus.
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The segmentation mask image is the same size and pixel resolution as the primary projection image and can be downloaded through the image download service.
Figure: Signal detection for projection data with injection in the primary motor area. Screenshot of a segmentation mask showing detected signal in the ventral posterolateral nucleus of the thalamus (VPL), internal capsule (int), caudoputamen (CP) and supplemental somatosensory area (SSs). In the Web application, the mask is color-coded for display: green indicates a pixel is part of an edge-like object while yellow indicates pixels that are part of a more diffuse region.
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% Download and unzip energy volume file for gene Rasd2 coronal SectionDataSet 73636089
mkdir('Rasd2_73636089');
urlwrite('http://api.brain-map.org/grid_data/download/74819249?include=density', 'temp.zip');
unzip('temp.zip','Rasd2_73636089');
% Download and unzip density volume file for BLAa injection SectionDataSet 113144533
mkdir('BLAa_113144533');
urlwrite('http://api.brain-map.org/grid_data/download/113144533?include=density', 'temp.zip');
unzip('temp.zip','BLAa_113144533');
% Gene expression grids are at 200 micron resolution.
geneGridSize = [67 41 58];
fid = fopen('Rasd2_73636089/density.raw', 'r', 'l' );
Rasd2 = fread( fid, prod(geneGridSize), 'float' );
fclose(fid);
Rasd2 = reshape( Rasd2, geneGridSize );
% Projection grids are at 100 micron resolution
projectionGridSize = [133 81 115];
fid = fopen('BLAa_113144533/density.raw', 'r', 'l' );
BLAa = fread( fid, prod(projectionGridSize), 'float' );
fclose(fid);
BLAa = reshape( BLAa, projectionGridSize );
% Upsample gene expression grid to same dimension as projection grid using linear interpolation
[xi,yi,zi] = meshgrid(1:0.5:41,1:0.5:67,1:0.5:58); %note: matlab transposes x-y
d = Rasd2; d(d<0) = 0; % fill in missing data as zeroes
Rasd2_100 = interp3(d ,xi,yi,zi,'linear');
% Handle "no data" (-1) voxels.
% Create a mask of "data" vs "no data" voxels and apply linear interpolation
m = zeros(size(Rasd2));
m(Rasd2 >= 0) = 1; mi = interp3(m,xi,yi,zi,'linear');
% Normalize data by dividing by interpolated mask. Assign value of "-1" to "no data" voxels.
Rasd2_100 = Rasd2_100 ./ mi;
Rasd2_100( mi <= 0 ) = -1;
% Create a merged image of one coronal plane;
gimg = squeeze(Rasd2_100(52,:,:)); gimg = max(0,gimg); gimg = gimg / 0.025; gimg = min(1,gimg);
pimg = squeeze(BLAa(52,:,:)); pimg = max(0,pimg); pimg = pimg / 0.8; pimg = min(1,pimg);
rgb = zeros([size(gimg),3]); rgb(:,:,1) = gimg; rgb(:,:,2) = pimg;
figure; image(rgb);
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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).
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Figure: Screenshot of source search results in the web application for experiments with injection in the isocortex. The injection location of each experiment is shown as a sphere on the 3D injection map.
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Figure: Screenshot of target search results in the web application for experiments with projection in target structure LGd (dorsal part of the lateral geniculate complex) and injection in the isocortex. The injection location of each experiment is shown as a sphere on the 3D injection map.
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Figure: Screenshot of spatial search results in the web application for experiments with projection in target location within VM (ventral medial nucleus of the thalamus). Each line in the 3D map is the computationally generated path from the target location to injection of one experiment.
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Figure: Screenshot of top returns of a correlation search for experiments with similar projection to a MOp injection experiment (top-left) within the thalamus