Spatial queries and the probe

From Whole Brain Catalog

Contents 1 Probe Tool Spatial Queries 1.1 Queries in the ABA (Allen Brain Atlas) 1.1.1 Get Fine Structure Name - ABA 1.1.2 Get Anatomic Structure Name - ABA 1.1.3 Transform Geometries to AGEA Space - ABA 1.1.4 Transform Geometries to WHS Space - ABA 1.1.5 Get 2D Image - ABA 1.1.6 Open Correlation Map - ABA 1.1.7 Get Genes - ABA 1.2 Queries in the WHS (Waxholm Space) 1.2.1 Get Structure Name - WHS 1.2.2 Transform Geometries to Paxinos Space – WHS

[edit] Probe Tool Spatial Queries

The probe tool can be used to launch spatial queries, including finding gene expression data from the Allen Brain Atlas. Bring up the Probe from the View menu. Once the probe is in your desired location, right-click on the probe and navigate through the context menu as shown to the left. This will bring up a page in your web browser with the appropriate gene expression data.

TIP: In order to get the probe where you want it, use the "my places" menu to get into the brain near where you want to be inside the brain. Then navigate from there.

The probe tool is also helpful in navigation.

[edit] Queries in the ABA (Allen Brain Atlas)

[edit] Get Fine Structure Name - ABA

This service returns the name(s) of segmented fine structures at the point of interest for Allen Brain Atlas space in a specified vocabulary. Currently, the service call returns a single structure. In the future, it will be extended to return a list of structures ranked by relevance, or proximity to the POI.

[edit] Get Anatomic Structure Name - ABA

This service returns the name(s) of segmented anatomic structures at the point of interest for Allen Brain Atlas space, in a specified vocabulary. Currently, the service call returns a single structure. In the future, it will be extended to return a list of structures ranked by relevance, or proximity to the POI.

[edit] Transform Geometries to AGEA Space - ABA

This service will find and execute the best transformation for Allen Brain Atlas coordinates from transformations available in the space_transformations resource, and returns the AGEA-based coordinates.

[edit] Transform Geometries to WHS Space - ABA

This service will find and execute the best transformation, for Allen Brain Atlas coordinates, from transformations available in the space_transformations resource, and returns the WHS-based coordinates.

[edit] Get 2D Image - ABA

This service returns an image from the Allen Brain Atlas space. The point of interest is calculated based on the location of the probe placed on the viewer and returns an image as an output that can be seen on the web browser.

[edit] Open Correlation Map - ABA

This service returns a map from the Allen Brain Atlas space. The point of interest is calculated based on the location of the probe on the viewer and returns an image as an output that can be seen on the web browser.

[edit] Get Genes - ABA

This service request will return genes from the Allen Brain Atlas space. The point of interest is calculated based on the coordinates on the probe placement within the client and returns back an image. The resulted images can be seen on the webpage.

[edit] Queries in the WHS (Waxholm Space)

[edit] Get Structure Name - WHS

This service returns name(s) of segmented fine structures as well as anatomic structures at the point of interest, in a specified vocabulary for WHS space. Currently, the service call returns a single structure. In the future, it will be extended to return a list of structures ranked by relevance, or proximity to the POI.

[edit] Transform Geometries to Paxinos Space – WHS

This service will find and execute the best transformation, for WHS coordinates, from transformations available in the space_transformations resource, and returns the Paxinos-based coordinates.