Global Text Search
Global Search helps you to filter your table data based on different categories like Injection Site, Tracers, Case Ids. You can select any category from the dropdown and type in some text that matches the selected category with the help of auto complete drop down.
Select a brain region to see a list of cases in which a tracer injection has been made in that location, e.g., Anterior Cingulate Cortical Area (ACA). Search can be performed by the full name or the acronym of the brain region according to the Allen Reference Atlas.
or select tracer for region of interest,
Anterograde tracers injected into a region of interest label the region's output projections. These tracers label axons and their terminal branches. Choose anterograde if you would like to view cases with anterograde tracers in your region of interest that show its output projections.
Retrograde tracers injected into a region of interest label all brain structures that provide input to the region. These tracers label the cell bodies of projection neurons that send inputs to the region of interest. Choose retrograde if you would like to view cases with retrograde tracers in your region of interest that show its input connections.
Project (# of cases)
Select the name of a project to get a list of its associated cases. For example, choosing Hippocampus will return all tracer injection cases that were used to assess the connectivity architecture of the hippocampus.
For select brain regions, in addition to connectivity information, gene expression data also is available through our collaborations with UCSD. The areas for which gene expression data is also available are indicated with the "insert symbol" symbol. Gene expression data for the region can be attained by clicking on "insert symbol".
- iConnectome: Total number of cases which are available to view in iConnectome Cell Type Viewer.
- Map: Total number of cases which are available to view in iConnectome Cell Type Map Viewer.
- Gene: Total number of cases which are available to view the gene expression data of the injection sites regions on UCSD web portal.
- Case ID
- Injection Site, Tracer, and ARA levels
- Projects and navigation buttons
- Image gallery
Navigating to viewers
iConnectome Cell Type Viewer
When you want to view a specific case on the iConnectome Viewer, click on the "case id" bubble will open up a new window to view the case of your interest.
You could also choose a multiple cases by clicking on the "case id" bubbles. Selected cases will appear on the right side panel. Once you click the view button, the iConnectome Cell Type Viewer will appear to view the cases of your selection.
iConnectome Cell Type Map Viewer
Navigation to the iConnectome Cell Type Map Viewer has two different options to view the labelings.
First, similar to the iConnectome Cell Type Viewer navigation, you can chose a specific interest of a case by clicking on a "case id" bubble. The bubble will open up a new window to view the case of your interest.
Second, you can pick the labels of the tracers of interested case(s). Selected cases will appear on the cart when the hamburger is clicked. After you verifies or change the combination of labelings to view, click on the view button and open a viewer window to view the combination of labelings.
Total cases: Total number of cases available on the Mouse Connectome Project data repository.
Injection sites: Total number of injection sites.
Pathways: Total number of projection pathways.
iConnectome: Total number of cases which are available to view in iConnectome Cell Type Viewer.
Map: Total number of cases which are available to view in iConnectome Cell Type Map Viewer.
Gene: Total number of cases which are available to view the gene expression data of the injection sites regions on UCSD web portal.