Versions Compared

Key

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

...

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:

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.

...

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:

Code Blocknoformat
http://api.brain-map.org/api/v2/data/WellKnownFile/query.xml?criteria=well_known_file_type[name$eq'ImagesResampledTo25MicronARA'][attachable_id$eq156198187]

 

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:

...

  • 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:

...

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:

...