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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.The aim of image alignment is to establish a mapping from each SectionImage to the 3-D reference space. The module reconstructs a 3-D Specimen volume from its constituent SectionImages and registers the volume to the 3-D reference model by maximizing mutual information between red channel of the experimental data and the average template.

Once registration is achieved, information from the 3-D reference model can be transferred to the reconstructed Specimen and vice versa. The resulting transform information is stored in the database. Each SectionImage has an Alignment2d object that represents the 2-D affine transform between a image pixel position to a location in the Specimen volume. Each SectionDataSet has an Alignment3d object that represents the 3-D affine transform between a location in the Specimen volume and point in the 3-D reference model. Spatial correspondence between any two SectionDataSets from different Specimens can be established by composing these transforms.

Image Added For convenience, a set of "Image Sync" API methods is available to find corresponding position between SectionDataSets, the 3-D reference model and structures. Note that all locations on SectionImages are reported in pixel coordinates and all locations in 3-D ReferenceSpaces are reported in microns. These methods are used by the Web application to provide the image synchronization feature in the multiple image viewer (see Figure).


  • Sync a VISp and VISal experiment to a location in a SCs SectionDataSet
  • Sync the P56 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.