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For convenience, a set of "Image Sync" API methods is available to find corresponding positions 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).
Examples:
Sync a VISp and VISal experiment to a location in a SCs SectionDataSet
No Format http://api.brain-map.org/api/v2/image_to_image/114754496.xml?x=18232&y=10704§ion_data_set_ids=113887162,116903968Sync the P56 coronal reference atlas to a location in the SCs SectionDataSet\
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No Format
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http://api.brain-map.org/api/v2/image_to_atlas/114754496.xml?x=18232&y=10704&atlas_id=1
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 red, green, and blue channels have been aligned to the 25um adult mouse brain reference space volume. These volumes have been stored in the API WellKnownFile table with type name "ImagesResampledTo25MicronARA". To retrieve the download link for a specific data set, query for WellKnownFiles of the appropriate type with an "attachable_id" equal to the data set id:
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http://api.brain-map.org/api/v2/data/WellKnownFile/query.xml?criteria=well_known_file_type[name$eq'ImagesResampledTo25MicronARA'][attachable_id$eq156198187]
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Download this by attaching the value of the download-link field to the API web host name (http://api.brain-map.org/api/v2/well_known_file_download/269830017). The download file will be a .zip file containing three images stored in the raw meta image format:
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Download projection_density for a VISal injection SectionDataSet (id=287495026) at 50 μm resolution
Code Blocknoformat http://api.brain-map.org/grid_data/download_file/287495026??image=projection_density&resolution=50
Example Matlab code snippet to read in the 50 µm projection_density grid volume and average_template:
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Projection statistics are encapsulated as a ProjectionStructureUnionize object associated with one Structure, either left, right or both Hemispheres and one SectionDataSet. ProjectionStructureUnionize can be downloaded via RMA. ProjectionStructureUnionize data is used in the web application to display projection summary bar graphs.
Examples:
No Format http://api.brain-map.org/api/v2/data/ProjectionStructureUnionize/query.xml?criteria=[section_data_set_id$eq126862385], [is_injection$eqfalse]&num_rows=5000&include=structureDownload injection site statistics for the same experiment
No Format http://api.brain-map.org/api/v2/data/ProjectionStructureUnionize/query.xml?criteria=[section_data_set_id$eq126862385], [is_injection$eqtrue]&num_rows=5000&include=structure- See the experiment detail page for the same experiment in the web application
- Take a look at the Cortico-thalamic Projection example application
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