Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  • projection density = sum of detected pixels / sum of all pixels in division
  • projection intensity = sum of detected pixel intensity / sum of detected pixels
  • projection energy = projection intensity * projection density

Wiki MarkupThe resulting 3-D grid is then transformed into the standard reference space.

Image Added Grid data can be downloaded for each SectionDataSet using the \[3-D Grid Data Service\](/doc/index. html#Downloading_3-D_Expression_Grid_Data). The service returns a zip file containing the volumetric data for density, intensity and/or energy in an uncompressed format with a simple text header file in [MetaImage|http://www.itk.org/Wiki/MetaIO/Documentation] format. Structural annotation for each grid voxel can be obtained via the ReferenceSpace [ gridAnnotation |http://iwarehouse/api/v2/well_known_file_download/159081322] volume file at 100 µm grid resolution.

Voxels with no data are assigned a value of "-1".

Examples:

Example Matlab code snippet to read in the 100 µm density grid volume:

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

  % 100 microngrid volume size
    sizeGrid = [133, 81, 115];

   % DENSITY = 3-D matrix of projection density grid volume
    fid = fopen('11_wks_coronal_126862385/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 (9573,:,:)));colormap(hot);caxis([0, 1]);colormap(hot);
    figure;imagesc(squeeze(DENSITY (:,:,7278)));colormap(hot);caxis([0, 1]);colormap(hot);

    

Projection Structure Unionization

Projection signal statistics can be computed for each structure delineated in the reference atlas by combining or unionizing grid voxels with the same 3-D structural label. While the reference atlas is typically annotated at the lowest level of the ontology tree, statistics at upper level structures can be obtained by combining measurements of the hierarchical children to obtain statistics for the parent structure. The unionization process also separates out the left versus right hemisphere contributions as well as the injection versus non-injection components.

Projection statistics are encapsulated as a ProjectionStructureUnionize object associated with one Structure, either left, right or both Hemispheres and one SectionDataSet.

Example:

ProjectionStructureUnionize data is used in the web application to display projection summary bar graphs.

Comparing Projection Data Grids and Gene Expression Grids

...

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).

Projection Structure Unionization

Projection signal statistics can be computed for each structure delineated in the reference atlas by combining or unionizing grid voxels with the same 3-D structural label. While the reference atlas is typically annotated at the lowest level of the ontology tree, statistics at upper level structures can be obtained by combining measurements of the hierarchical children to obtain statistics for the parent structure. The unionization process also separates out the left versus right hemisphere contributions as well as the injection versus non-injection components.

Projection statistics are encapsulated as a ProjectionStructureUnionize object associated with one Structure, either left, right or both Hemispheres and one SectionDataSet.

Example:

ProjectionStructureUnionize data is used in the web application to display projection summary bar graphs.