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- projection density = sum of detected pixels / sum of all pixels in division
- projection energy = sum of detected pixel intensity / sum of all pixels in division
- injection_fraction = fraction of pixels belonging to manually annotated injection site
- injection_density = density of detected pixels within the manually annotated injection site
- injection_energy = energy of detected pixels within the manually annotated injection site
- data_mask = xxxxxxbinary mask indicating if a voxel contains valid data (0=invalid, 1=valid)
For each summation type, grid files can be downloaded at 10, 25, 50 and 100 μm isotropic voxel resolution.
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% ------------------------------- % % Download a NRRD reader % For example: % http://www.mathworks.com/matlabcentral/fileexchange/34653-nrrd-format-file-reader % % Requires: MATLAB 7.13 (R2011b) % % Download average_template_50.nrrd % Download projection_density at 50 micron for SectionDataSet id = 287495026 % % --------------------------------- % % Read image volume with NRRD reader % Note that reader swaps the order of the first two axes % % AVGT = 3-D matrix of average_template % PDENS = 3-D mstrixmatrix of projection_density % DMASK = 3-D matrix of data_mask % [AVGT, metaAVGT] = nrrdread('average_template_50.nrrd'); [PDENS, metaPDENS] = nrrdread('11_wks_coronal_287495026_50um_projection_density.nrrd'); [DMASK, metaDMASK] = nrrdread('11_wks_coronal_287495026_50um_data_mask.nrrd'); % Display one coronal section figure;imagesc(squeeze(AVGT(:,184,:)));colormap(gray(256)); axis equal; figure;imagesc(squeeze(PDENS(:,184,:)));colormap(jet(256)); axis equal; figure;imagesc(squeeze(DMASK(:,184,:)));colormap(gray(256)); axis equal; |
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